Supplementary materials - Stanford Artificial Intelligence Laboratory

Transcription

Supplementary materials
Genetic regulatory network of modules (Geronemo)
As discussed in the paper, the Geronemo learning algorithm iterates over two phases: (1)
assigning each gene into some regulatory module; (2) learning the regulation program for
each module. At a high level, our method follows the module network approach of Segal et
al. (1). However, as discussed in the paper, we introduced several important innovations
that are keys to the success of the method in this new setting. Below, we review both the
module network procedure and our extensions.
1. Regulation programs
We adopted the concept of the regulation program from Segal et al. (1). Briefly reviewing,
a regulation program of a gene G specifies a set of contexts and G’s expression values in
each context. A context corresponds to a regulation state of G determined by the qualitative
behavior of a small set of regulatory factors that control G’s expression. This set of contexts
is organized as a regression tree in which each path to a leaf in the tree defines a context
using the tests on the path. A regression tree is composed of two basic building blocks:
decision nodes and leaf nodes. Each decision node corresponds to one of the regulatory
inputs and a query on its value (for example, "is Hap1 up-regulated?"). Each decision node
has two child nodes: the right child node is chosen when the answer to the corresponding
query is true; the left node is chosen when not. For a gene in a given array, one begins at
the root node and continues down the tree in a path according to the answers to the queries
in that particular array. Thus, each leaf (context) corresponds to the arrays that traverse the
same path through the tree. The response of the gene in each context is modeled as a
normal distribution over the expression values of the gene in the corresponding individuals;
this distribution is encoded using a mean and variance stored at the corresponding leaf. The
model semantics is that, given a gene G and an array A in a context, the probability of
observing some expression value for gene G in an array A is governed by the normal
distribution specified for that context. For a context in which the expression values are
tightly regulated, the distribution may have a small variance; in a context where the
expression values are not tightly regulated, the distribution may have a large variance. In
the current study, we allowed two types of regulatory factors: the genotype of some
chromosomal region defined by a marker, which (in our data) has two possible split values,
for the two progenitor alleles; and the expression level of some regulator R, whose set of
possible splits is the number of different continuous values that the regulator takes on in the
expression arrays.
2. Geronemo learning algorithm
Learning a Geronemo model involves two tasks: (1) assigning each gene into some
regulatory module; (2) learning the regulation program for each module. We initialized the
learning procedure with 500 modules obtained by k-means clustering, and then iterated
over two phases: learning the regulatory program for the current modules, and re-assigning
genes to modules. In our learning procedure, we prevented genes from regulating the same
module in which they appeared, but did not require global acyclicity because the real
regulatory network is not acyclic.
(a) Learning the regulatory program: Given a set of modules, we learned the regulatory
association for each module by using the candidate expression (e-) and genotype (g-)
regulators as candidate genetic regulators. As described above, the association between the
genetic regulators and the expression of genes can be represented as a regression tree. We
learned the tree by adding a decision node to a context. The first added node becomes the
root that creates two contexts, and we search for the candidate regulators that can make the
decision node for those two contexts. When considering adding a decision node to the
regulatory program of each module, we considered all candidate genetic regulators and split
values and picked the pair (genetic regulator, split value) that achieves the highest delta
score, i.e., the difference of the score (see below) after adding the decision node
corresponding to the pair. We stopped adding the decision node when adding a decision
node does not increase the score.
Importantly, the candidate genetic regulators for Geronemo consist of both continuousvalued e-regulators and discrete-valued g-regulators. The continuous-valued candidate
regulators have more possible split values than the discrete-valued ones; therefore it is
possible that e-regulators can be captured more often than g-regulators due to the spurious
correlation with the genes in the module. We extended our learning scheme to correct for
these effects. When considering adding a decision node to the regulatory program, we take
the following steps. (1) We first choose the e-regulator that achieves the highest score
among all candidate e-regulators, and the g-regulator with the highest score among all
candidate g-regulators. (2) For each of the highest-scoring e- and g- regulator, we carried
out 1,000 permutation tests and calculated the false discovery rate (FDR), i.e., the
frequency with which the score is higher than the original one among the 1,000 randomly
permuted data. To ensure that it is the expression value of an e-regulator which is predictive,
we permute its expression values within each of its genotypes separately. (3) We select
either the e- or g- regulator with the lower FDR. If the chosen FDR is > 0.05, we select the
next highest scoring regulator, and repeat. If the top 3 regulators in e- and g- regulator
groups have FDR > 0.05, the process terminates.
(b) Learning the module assignment: We iterate over all genes one at a time, for each one
moving it into the module Mj that provides the highest improvement in the score (see
below). We repeated this re-assignment process over all genes three times. To allow for cisregulation effects, which often result in modules containing only a very small number of
genes, we introduced a step that allows genes to “break off” from their module and create a
new one. When the module assignment is stabilized to some extent (when the number of
genes moved < 200), we considered a singleton decision step for each gene gi,, as follows:
Let Mj be the current module of gi; we consider breaking Mj into two modules – a module Si
containing only gi, and a module Mj’ containing the rest of the genes in Mj. We then decide
whether to accept the new split by comparing the scores of the pre-split and post-split
models. To avoid over-fitting, in the post-split model, the regulation trees of Si and Mj’
(required for computing the score) are learned using only the genetic regulators and their
split values used in the regulation program of Mj, and, for Si, also allowing gi’s genotype as
a parent.
(c) Score function: We use a Bayesian scoring approach, which tries to maximize the
overall joint probability of the model and the data. The score consists of two parts: the
marginal data and the prior probability of the model structure. The marginal data
likelihood is simply log ∫ P( D | S , R, θ ) P (θ )dθ , where the parameter prior P(θ ) is a
θ
normal-gamma distribution that depends on two parameters ( α and ε ), which determines
the strength of the regularization. We also have a complexity prior over regulation
programs, P( R) ∝ exp − βn , where n is the total number of leaves in the regulation trees. To
bias the model in favor of more biologically plausible regulation programs, we also
introduced a prior distribution P(S) on model structures that imposes sparsity both on the
number of targets of each regulator, and on the number of distinct split-values that a
regulator has. This prior takes the form of a power-law distribution on the number of transtargets of the genetic regulators, and on pairs of (regulator, split value):
P( S ) ∝
(∏
(p,s)∈{all pairs of P and S}
[w( p, s) + 1])− x (∏p∈{all genetic regulators} [w( p) + 1])− y ,
where w(p,s) represents the number of trans-regulated targets of the regulator p with the
∑ w(p, s) .
split value s, and w(p) =
s∈{all split valu es of p}
This prior helps avoid overfitting, especially for small modules (consisting of <3 genes).
Overall, we have the following score:
log P( D, S , R ) = log P( D | S , R ) + log P ( S ) + log P ( R)
= log ∫ P( D | S , R,θ ) P(θ )dθ −x
θ
−y
∑ log{w(p, s) + 1}
(p,s)∈{all paris of (trans- regulator, split value) }
∑ log{w(p) + 1} − βn
p∈{all trans - regulators}
The parameters of the score ( β , α , ε , x and y) were determined by optimizing the loglikelihood of test data, using 5-fold cross-validation.
Enrichment analysis for number of polymorphisms in a gene group
As we discussed in the paper, we applied an enrichment analysis of polymorphisms for
several groups of genes: cis-genes, regulators in the vicinity of markers selected as parents,
and the genes in the Swi/Snf complex. For coding sequences, we evaluated enrichment for
non-synonymous SNPs, and for promoter regions, we evaluated enrichment for any SNPs,
taking the regions to include the 500bp upstream of the transcription start site. In either case,
we computed enrichment of the polymorphisms in a gene group of interest (case group) by
comparing the distribution of the number of polymorphisms between the group and a
control group. The control group consisted of the genes that are adjacent (one upstream and
one downstream) to the genes in the group of interest. The distribution of the number of
polymorphisms is far from any standard distribution used in general statistical hypothesis
tests. Therefore, we devised a non-parametric false discovery rate correction method that
evaluates significance using 1,000 permutation tests. In each case group S, we computed
the hyper-geometric enrichment of the case group, relative to the control group, for genes
that contain >n polymorphisms. We varied n such that the p-value based on the hypergeometric distribution is minimized. If such minimum p-value is smaller than 0.01, we
performed 10,000 permutation tests to verify the significance. In each permutation test i, we
chose a “random case group” Si with the same number of genes as S, and defined the
control group to be the genes adjacent to Si. We then varied the cutoff n in the same way,
and calculated the p-value. The FDR-corrected p-value is the fraction of permutation tests
where the p-value of the random case group Si is smaller than that of S.
Proportion of genetic variance explained by genetic regulators
We carried out an unbiased estimation of the percentage of genetic variance (PGV)
explained by the identified genetic regulators (2), using a method analogous to that of Brem
and Kruglyak (3). We randomly divided the data of 112 segregants into two sets of the
same size (56 segregants): the detection set and the estimation set. Using the detection set,
we identified the regulation program through our procedure (Supplementary Fig. 1). Then,
we used the estimation set to calculate the PGV on the basis of the identified regulation
programs. The PGV of a gene G is defined as
PGVG =
2
R adj
(e G , g G )
ĥ G2
× 100 .
The denominator ĥ G2 is the heritability of G, defined as ĥ 2 = (σ s2 - σ p2 )/σ s2 ,
Where σ s2 and σ p2 are the variance among its expression values in the segregants and its
2
pooled variance among parental measurements, respectively. The numerator R adj
(e G , g G )
is the adjusted squared correlation coefficient between the expression values of G in the
estimation set ( e G ) and predicted expression values for G based on the learned regulation
program ( g G ). This term is defined using single-factor ANOVA, where the factors are the
contexts learned from the detection set. Thus, we took the learned regulation program from
the detection set, used the contexts it identifies (leaves in the regulation tree) to estimate eG,
2
(e G , g G ) accordingly, as:
and computed R adj
2
R adj
(e G , g G ) = R 2 − (
z
)(1 − R 2 ) ,
N − z −1
where R2 is the square correlation coefficient between eG and gG, z is the number of
contexts of the regulation program and N is the number of expression values in the
estimation set which is determined by multiplying the number of individuals in the
estimation set by the number of genes in the module. Note that Radj corrects not only for the
number of contexts in the regulatory programs (by z term), but also for the module-based
models (by N term) because theoretically, this test is harder for the module-based models
that force sharing of the parameters of the genes in the same module..As in the work of
Brem & Kruglyak. (3), if PGV was <0, we assigned it to be identically 0, if it was >1, we
excluded it; genes with estimated heritabilities <0 were also excluded.
We repeated this detection/estimation process 10 times with different random splits of data,
and computed PGVg for each gene by taking the average of PGV of the gene over 10 runs.
If the gene is not assigned a regulatory program in a run, we considered its PGV in that run
to be 0. In Supplementary Fig. 2, we plotted PGVg (y-axis) of 3,152 genes (x-axis) used in
our analysis and sorted by their PGVg’s. We also plotted the result reported by Brem &
Kruglyak (3) who conducted the same experiment to calculate the PGV’s in 10 runs, each
of which detected a linkage for 1,038 genes on average, and presented the fraction of
PGVs’ in given ranges (red boxes). Note that, in Supplementary Fig.2, the number of genes
corresponding to each PGV range was estimated by multiplying the average number of
genes detected in each run (1,038) by the fraction for the PGV range they reported.
Annotation Enrichment
We evaluated the biological relevance of each regulatory module in the context of other
genomic datasets. We used the hyper-geometric p-value to test for functional enrichment
of 1601 GO categories taken from SGD (4). To associate transcription factors (and
sometimes their known upstream signaling molecule) to targets we used ChIP binding
data for transcription factors (5) and chromatin modifying factors (6)(7) and used a pvalue < 0.001 cutoff to define a target set for each regulator. For the Isw2 protein (7), we
considered the genes whose log2 ratio of IP/input >1 to be Isw2 targets. We also used a
map of putative TF binding sites (motifs) for 65 motifs from the Fraenkel lab website (5).
We took the union of binding sites conserved in at least 2 other yeast species and
binding sites that match the Harbison et al. (5) binding data. We used the resulting motif
map both to test for enrichment in our modules and for the actual location of the
predicted binding site to mark SNPs potentially perturbing a transcription factor binding
site. As an additional resource for associating regulators to (not necessarily direct)
targets we used differentially expressed genes (DEGs) from deletion mutants of different
regulators in (8-10). For each deletion we defined a threshold for differentially
expressed as described in (11). For the full set of annotations (function, binding data and
DEG targets), we removed all annotations associated with less than five genes from our
gene set. For each module and each annotation, we counted the number of predicted
target genes associated with that particular annotation, and calculated a p-value by using
the hyper-geometric distribution. We carried out a false discovery rate (FDR) correction
for multiple independent hypotheses and took values of Pcorrected < 0.005 to be significant.
Identifying orthologous genes between BY and RM
We downloaded the genome sequences of S288C (isogenic to BY) and RM from the
Saccharomyces Genome Database (4) and Broad Institute of Fungal Genome Initiative (12),
respectively (sequences were retrieved on 12 January 2005). In order to define orthologous
genes between BY and RM, we used reciprocal best BLAST hit (13) (protein sequences of
S288C were download from SGD(4) on 12 January 2005). We retrieved the genomic
sequences, 500 bp upstream of each orthologous pair, and aligned them by using
LAGAN(14). Out of 6683 genes in 16 nuclear chromosomes, 6292 (94.1493%) have
reciprocal best matches between the two strains.
Positive selection test for regulatory GO categories
We checked the enrichment for the genes that are likely to be under positive selection in 38
GO categories related to various regulatory roles. We collected 1097 genes with dN>dS
from the dN-dS test (15) and 38 GO categories related to any regulatory role. For each GO
category, we computed the p-values representing the significance of the overlap between
the genes with dN>dS and the genes belonging to the category. We sorted the categories
and listed below. As we discussed in the paper, Swi/Snf complex is the only category with
the p-value<0.01.
Gene Ontology category
p-value
SWI/SNF complex
0.001471
#Genes
with
dN>dS
in (1)
6
#Genes (2)
(1)
Others
with
GO
genes dN>dS
in (2)
11
1091
5726
Regulation of meiosis
Regulation of transcription from RNA
polymerase II promoter
Specific RNA polymerase II transcription
factor activity
Chromatin remodeling complex
Histone acetyltransferase complex
Transcriptional activator activity
Rho protein signal transduction
Protein tyrosine phosphatase activity
SAGA complex
Specific transcriptional repressor activity
H4/H2A
histone
acetyltransferase
complex
Histone deacetylase complex
Chromatin remodeling
Protein serine/threonine kinase activity
Transcriptional repressor activity
Regulation of transcription, DNAdependent
Protein kinase activity
General RNA polymerase II transcription
factor activity
Chromatin silencing at telomere
Regulation of cyclin dependent protein
kinase activity
Chromatin silencing at ribosomal DNA
Transcription factor activity
RNA polymerase II transcription factor
activity
Transcription coactivator activity
Transcription corepressor activity
GTPase activity
Histone acetyltransferase activity
Histone deacetylase activity
Signal transducer activity
DNA-directed RNA polymerase II, core
complex
Chromatin silencing
Transcription
Transcription from RNA polymerase II
promoter
0.015522
5
12
1092
5725
0.015599
20
69
1077
5668
0.037232
0.04219
0.050093
0.069418
0.088299
0.105621
0.111913
0.141865
12
4
5
9
5
3
5
3
41
11
15
32
17
10
18
11
1085
1093
1092
1088
1092
1094
1092
1094
5696
5726
5722
5705
5720
5728
5719
5726
0.141865
0.211988
0.23467
0.287139
0.295709
3
4
11
7
2
11
17
50
33
10
1094
1093
1086
1090
1095
5726
5720
5687
5704
5727
0.311781
0.327968
6
10
29
49
1091
1087
5708
5688
0.3505
0.381095
8
8
40
41
1089
1089
5697
5696
1
1
1
2
0
7
14
12
57
1095
1097
1090
5723
5725
5680
1
1
1
1
1
1
1
1
1
3
10
1
2
3
17
11
16
57
14
11
23
1096
1096
1094
1088
1096
1095
1094
5720
5726
5721
5681
5723
5726
5714
1
1
1
1
1
3
11
16
29
1096
1096
1094
5726
5721
5708
1
4
40
1093
5697
Signal transduction
Small
GTPase
mediated
transduction
Ras protein signal transduction
Chromatin modification
1
5
36
1092
5701
1
1
1
4
1
3
21
14
19
1094
1096
1094
5717
5723
5718
signal
Figure legends
Supplementary Figure 1: Overview of Geronemo algorithm.
Geronemo (see description above) takes as input data a set of individuals in a population,
measuring both their gene expression profiles and chromosomal markers. Additionally, it
takes a large precompiled set of candidate regulators. After an initial partitioning of genes
into modules, the procedure iteratively applies two phases until convergence: (right) for
each module, the method searches for a regulation program; (left) after identifying a
regulation program for each module, the procedure reassigns each gene to the module
whose program best predicts the gene’s behavior. The resulting modules provide a
mechanistic explanation of the regulatory network and the perturbations to it induced by
sequence variation.
Supplementary Figure 2: Variance explained by different variants of Geronemo and
by eQTL analysis
The percentage of genetic variation (PGV) explained by detected genetic factors (2), for
Geronemo (pink) and three simpler variants of Geronemo, and for the extended eQTL
analysis method of Brem & Kruglyak (3) applied to the same dataset (red boxes). We
generated 10 randomly partitioned detection/estimation sets. For each set, we identified the
associations with the detection set, and then we used the estimation set to calculate PGV for
each gene on the basis of the identified regulation programs (see description above). For
each gene, we determined PGVg by taking the average of the PGV values for the gene over
the 10 datasets. The graph shows the PGVg values (y-axis) of 3152 genes (x-axis). The
genes (x-axis) are sorted by their PGVg; thus, x-axis represents the number of genes with
PGVg greater than the the corresponding y-axis value. The data for the eQTL method (red
boxes) are based on the ranges reported by Brem and Kruglyak (3), using the same
procedure. The simpler variants of Geronemo consist of three models: (1) allowing only
markers as genetic regulators (ModuleReg-G; blue), (2) forcing each gene to form a
separate module (SingleReg-G/Reg-E; sky blue), and (3) both of the constraints
(SingleReg-G; yellow). A significant advantage is obtained by explicitly modeling
regulatory effects by the expression values of regulators, and module-based models show
higher PGV than the corresponding single gene-based models. Note that the module-based
models identified more genetic regulators per gene than the single gene-based model
(ModuleReg-G/Reg-E: 5.25, ModuleReg-G: 6.09, SingleReg-G/Reg-E: 1.36, SingleReg-G:
2.14). This suggests that the module-based model achieves stronger statistical power by
detecting more intricate combinatorial interaction.
Supplementary Figure 3: Nucleosome module
This module is enriched for histones and includes many other cell cycle regulated genes.
(i) The module’s regulatory program: Apg1, the top regulator is itself regulated by Fkh1
and Swi6, as are many other regulators in the program. (ii) Relevant annotations for the
module genes. The module is enriched with targets of a number of cell cycle regulators:
Swi4 (p<8.79x10-10), Mpb1 (p<1.2x10-8), Swi6 (p<7.9x10-8) and Fkh1 (p<7x10-4) targets.
The genes marked in pink are histones (p<1x10-8). (iii). Expression data for the module
genes.
Supplementary Figure 4: Cell cycle regulation of histones
This figure represents the cell-cycle dependent co-regulation program of 8 histone genes
(blue nodes) that appear in the nucleosomal module (#40). These are known to be regulated
by 4 transcription factors (yellow nodes) that regulate the G1 to S transition of the cellcycle. Histones in yeast are known to be transcriptionally regulated in a cell-cycle
coordinated manner, with RNA expression peaking in S phase, when large amounts of
histones are needed for assembly into newly synthesized DNA (16). An edge from a
transcription factor to another node means the target gene has a binding site for that factor
(5). A red edge means that there is genetic variation in these binding sites between BY and
RM. In RM, there are several SNPs and gaps directly in the predicted binding sites of these
cell-cycle regulators. The common promoter of Hhf1-Hht1 has close to 500 SNPs that
remove two binding sites of both Swi6 and Fkh1; the promoter of Hta2-Htb2 also has a
SNP in one of the binding sites for Mbp1 and Swi6. Interestingly, the cell cycle dependent
regulatory network upstream of these transcription factors seems to have also been
modulated. The G1 cyclin Cln2 activates the catalytic subunit of the main cell cycle cyclindependent kinase Cdc28, which in turn activates both Fkh1 and Swi6. Cln2 and Cdc28 also
have SNPs in their regulatory program, Cln2 in a Swi4 binding site and Cdc28 in an Fkh1
binding site. Our results suggest that these natural variants exhibit differential regulation of
the G1/S transition, perhaps involving timing, and that the mechanisms underlying this
perturbation are cis-regulation of key cell-cycle regulators and of histone proteins.
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Supplementary Fig. 1
Yeast recombinants
…
ORFs
:
:
Expression data
…
…
Markers
:
Candidate
Regulators
:
Genotype data
…
Geronemo learning procedure
Module assignment
Initializing module
assignment
:
Constructing
regulatory program
:
:
:
Repeat until
convergence
:
Mechanistic explanation
Zap1-E
Zap1-G
Zap1
expression
Zap1
genotype Zap1 has a coding SNP
whose BY (blue) variant
represses its targets.
:
Single
Reg-G/Reg-E
PGV (%)
Module
Reg-G/Reg-E
Module
Reg-G
Single
Reg-G
Brem et al.
(2005)
Genes
Rpb8-E
Kar4-E
Sip4-E
(iii)
Kar4-E
Caf17-E
Fkh1 binding sites (p<7.04e-4)
Swi6 binding sites (p<8.87e-8)
(i)
Swi4 binding sites (p<8.79e-10)
Mbp1 binding sites (p<1.16e-8)
Apg1-E
Ask10-E
(ii)
Histone in module
Transcription Factor
Upstream Signaling
Cdc28
Binds to
Altered binding site
p-p interaction
Cln2
Mbp1
Htb2
Swi6
Fkh1
Swi4
Hta2
Hhf2
Hht2
Htb1
Hta1
Hhf1
Hht1
Table 1: 304 candidate regulators
We used a precompiled list of 304 putative regulators, spanning transcription factors, signal
transduction proteins, chromatin modification factors, and mRNA processing factors.
ORF name
Gene
name
YAL017W
PSK1
YAL040C
CLN3
YAL056W
GPB2
YBL002W
HTB2
YBL003C
HTA2
YBL005W
PDR3
YBL008W
HIR1
YBL009W
YBL00
9W
YBL016W
FUS3
YBL052C
YBL066C
SAS3
SEF1
YBL084C
CDC27
YBL103C
RTG3
YBR009C
HHF1
YBR010W
HHT1
YBR026C
ETR1
YBR045C
GIP1
SGD description
One of two (see also PSK2) PAS domain containing S/T protein kinases;
coordinately regulates protein synthesis and carbohydrate metabolism and
storage in response to a unknown metabolite that reflects nutritional status
role in cell cycle START; involved in G(sub)1 size control; G(sub)1 cyclin
Proposed beta subunit of the heterotrimeric G protein that interacts with the
receptor Grp1p, has signaling role in response to nutrients; involved in regulation
of pseudohyphal growth through cAMP levels; homolog of Gpb1p
One of two nearly identical (see HTB2) histone H2B subtypes required for
chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated
ubiquitination regulates transcriptional activation, meiotic DSB formation and H3
methylation
One of two nearly identical (see also HTA1) histone H2A subtypes; core histone
required for chromatin assembly and chromosome function; DNA damagedependent phosphorylation by Mec1p facilitates DNA repair; acetylated by
Nat4p
Transcriptional activator of the pleiotropic drug resistance network, regulates
expression of ATP-binding cassette (ABC) transporters through binding to cisacting sites known as PDREs (PDR responsive elements)
Non-essential transcriptional corepressor involved in the cell cycle-regulated
transcription of histone H2A, H2B, H3 and H4 genes; contributes to nucleosome
formation, heterochromatic gene silencing, and formation of functional
kinetochores
Mitogen-activated protein kinase (MAPK) involved in mating pheromone
response; activated by phosporylation by Ste7p; controls different aspects of the
mating response by phosphorylating transcriptional and cytoplasmic targets
Protein involved in silencing at HMR
Suppressor of Essential Function; putative transcription factor
Subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a
ubiquitin-protein ligase required for degradation of anaphase inhibitors, including
mitotic cyclins, during the metaphase/anaphase transition
Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms
a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde
(RTG) and TOR pathways
One of two identical histone H4 proteins (see also HHF2); core histone required
for chromatin assembly and chromosome function; contributes to telomeric
silencing; N-terminal domain involved in maintaining genomic integrity
One of two identical histone H3 proteins (see also HHT2); core histone required
for chromatin assembly, involved in heterochromatin-mediated telomeric and
HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation
2-enoyl
thioester
reductase,
member
of
the
medium
chain
dehydrogenase/reductase family; localized to in mitochondria, where it has a
probable role in fatty acid synthesis
Meiosis-specific protein proposed to be a regulatory subunit of the protein
YBR049C
REB1
YBR050C
REG2
YBR059C
AKL1
YBR066C
NRG2
YBR073W
RDH54
YBR083W
TEC1
YBR098W
MMS4
YBR103W
SIF2
YBR112C
CYC8
YBR125C
PTC4
YBR136W
MEC1
YBR140C
IRA1
YBR150C
TBS1
YBR158W
AMN1
YBR160W
CDC28
YBR175W
SWD3
YBR182C
SMP1
YBR193C
MED8
YBR195C
MSI1
YBR203W
YBR212W
YBR240C
COS11
1
NGR1
THI2
phosphatase Glc7p, required for spore wall formation and proper septin
organization
RNA polymerase I enhancer binding protein; DNA binding protein which binds
to genes transcribed by both RNA polymerase I and RNA polymerase II;
required for termination of RNA polymerase I transcription
Protein that binds type 1 protein phosphatase Glc7p; involved with Reg1p,
Glc7p, and Snf1p in regulation of glucose-repressible genes
Serine-threonine protein kinase, member (with Ark1p and Prk1p) of the Ark
kinase family
Transcriptional repressor that mediates glucose repression and negatively
regulates filamentous growth; has similarity to Nrg1p
genetic interaction with DMC1; Putative helicase similar to RAD54
transcription factor of the TEA/ATTS DNA-binding domain family, regulator of
Ty1 expression
endonuclease
Sir4p-Interacting Factor; 535 amino acid protein containing 4 WD-40 repeats and
a nuclear localization signal
General transcriptional co-repressor, acts together with Tup1p; also acts as part
of a transcriptional co-activator complex that recruits the SWI/SNF and SAGA
complexes to promoters
Phosphatase type Two C; Type 2C protein phosphatase
Central regulator of the Mec1p/Tel1p signaling network; required for mitotic
growth, DNA repair and mitotic recombination, regulates phosphorylation of
Rad53p, required for dmc1 arrest and meiotic recombination; similar to
phosphatidylinositol(PI)3-kinases required for DNA damage induced checkpoint
responses in G1, S/M, intra S, and G2/M in mitosis
GTPase-activating protein that negatively regulates RAS by converting it from
the GTP- to the GDP-bound inactive form, required for reducing cAMP levels
under nutrient limiting conditions, mediates membrane association of adenylate
cyclase
Probable Zn-finger protein
Involved in daughter cell separation and Chromosome STability; Chromosome
STability
Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK);
alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which
direct the CDK to specific substrates
Subunit of the COMPASS complex, which methylates histone H3 on lysine 4 and
is required in transcriptional silencing near telomeres
Transcription factor of the MADS (Mcm1p, Agamous, Deficiens, SRF) box
family; closely related to RLM1; Probable DNA-binding transcription factor,
Homolog to SRF/SL-2
Member of RNA Polymerase II transcriptional regulation mediator;
Stoichiometric member of mediator complex
Subunit of chromatin assembly factor I (CAF-I), regulates the RAS/cAMP
pathway via sequestration of Npr1p kinase; localizes to the nucleus and
cytoplasm; homologous to human retinoblastoma binding proteins RbAp48 and
RbAp46
Protein required for wild-type resistance to the antifungal drug ciclopirox
olamine; not related to the COS family of subtelomerically-encoded proteins
negative growth regulatory protein
Zinc finger protein of the Zn(II)2Cys6 type, probable transcriptional activator of
YBR245C
ISW1
YBR274W
CHK1
YBR278W
DPB3
YBR297W
MAL33
YCL024W
KCC4
YCL026C-A
FRM2
YCL055W
KAR4
YCL066W
HMLA
LPHA1
YCL067C
HMLA
LPHA2
YCR039C
MATA
LPHA2
YCR040W
MATA
LPHA1
YCR065W
HCM1
YCR073C
SSK22
YCR091W
KIN82
YCR097W
HMRA
1
YCR106W
RDS1
YDL017W
CDC7
YDL020C
RPN4
YDL025C
YDL02
thiamine biosynthetic genes
Member of the imitation-switch (ISWI) class of ATP-dependent chromatin
remodeling complexes; ATPase that forms a complex with Ioc2p and Ioc4p to
regulate transcription elongation, and a complex with Ioc3p to repress
transcription initiation
checkpoint kinase 1; homolog of the S. pombe and mammalian Chk1 checkpoint
kinases; Protein kinase Chk1
Third-largest subunit of DNA polymerase II (DNA polymerase epsilon), required
to maintain fidelity of chromosomal replication and also for inheritance of
telomeric silencing; mRNA abundance peaks at the G1/S boundary of the cell
cycle
MAL-activator protein, part of complex locus MAL3; nonfunctional in genomic
reference strain S288C
Protein kinase of the bud neck involved in the septin checkpoint, associates with
septin proteins, negatively regulates Swe1p by phosphorylation, shows structural
homology to bud neck kinases Gin4p and Hsl1p
Protein of unknown function, involved in the integration of lipid signaling
pathways with cellular homeostasis
Transcription factor required for induction of KAR3 and CIK1 during mating,
also required during meiosis; exists in two forms, a slower-migrating form more
abundant during vegetative growth and a faster-migrating form induced by
pheromone
Silenced copy of ALPHA1, encoding a transcriptional coactivator involved in the
regulation of mating-type alpha-specific gene expression
Silenced copy of ALPHA2, encoding a homeobox-domain containing protein
that associates with Mcm1p in haploid cells to repress a-specific gene expression
and interacts with A1p in diploid cells to repress haploid-specific gene expression
Homeobox-domain containing protein which, in haploid cells, acts with Mcm1p
to repress a-specific genes; in diploid cells Alpha2p acts together with A1p to
repress transcription of haploid-specific genes
Transcriptional co-activator involved in regulation of mating-type-specific gene
expression; targets the transcription factor Mcm1p to the promoters of alphaspecific genes; one of two genes encoded by the alpha mating type cassette
Forkhead transcription factor involved in cell cycle specific transcription of
SPC110, encoding a spindle pole body (SPB) calmodulin binding protein;
dosage-dependent suppressor of calmodulin mutants with specific defects in SPB
assembly
functionally redundant with, and homologous to, SSK2; protein kinase
Putative serine/threonine protein kinase, most similar to cyclic nucleotidedependent protein kinase subfamily and the protein kinase C subfamily
Silenced copy of A1, encoding a homeobox-domain containing corepressor that
interacts with Alpha2p to repress haploid-specific gene transcription in diploid
cells
Regulator of drug sensitivity; transcriptional regulator
DDK (Dbf4-dependent kinase) catalytic subunit required for firing origins and
replication fork progression in mitosis through phosphorylation of Mcm2-7p
complexes and Cdc45p; kinase activity correlates with cyclical DBF4 expression
Transcription factor that stimulates expression of proteasome genes; Rpn4p
levels are in turn regulated by the 26S proteasome in a negative feedback control
mechanism; RPN4 is transcriptionally regulated by various stress responses
5C
YDL064W
UBC9
YDL101C
DUN1
YDL106C
PHO2
YDL170W
UGA3
YDL214C
PRR2
YDL230W
PTP1
YDL248W
COS7
YDR009W
GAL3
YDR034C
LYS14
YDR043C
NRG1
YDR075W
PPH3
YDR085C
AFR1
YDR121W
DPB4
YDR145W
TAF12
YDR195W
REF2
YDR213W
UPC2
YDR216W
ADR1
YDR223W
CRF1
YDR224C
HTB1
YDR225W
HTA1
SUMO-conjugating enzyme involved in the Smt3p conjugation pathway; nuclear
protein required for S- and M-phase cyclin degradation and mitotic control;
involved in proteolysis mediated by the anaphase-promoting complex cyclosome
(APCC)
Cell-cycle checkpoint serine-threonine kinase required for DNA damage-induced
transcription of certain target genes, phosphorylation of Rad55p and Sml1p, and
transient G2/M arrest after DNA damage; also regulates postreplicative DNA
repair
Homeobox transcription factor; regulatory targets include genes involved in
phosphate metabolism; binds cooperatively with Pho4p to the PHO5 promoter;
phosphorylation of Pho2p facilitates interaction with Pho4p
Transcriptional activator necessary for gamma-aminobutyrate (GABA)dependent induction of GABA genes (such as UGA1, UGA2, UGA4); zincfinger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type
Protein kinase with a possible role in MAP kinase signaling in the pheromone
response pathway
phosphotyrosine-specific protein phosphatase
Protein of unknown function, member of a family of conserved, often
subtelomerically-encoded proteins
Transcriptional regulator involved in activation of the GAL genes in response to
galactose; forms a complex with Gal80p and Gal4p to relieve inhibition by
Gal80p; binds galactose and ATP but does not have galactokinase activity
Transcriptional activator involved in regulation of genes of the lysine
biosynthesis pathway; requires 2-aminoadipate semialdehyde as co-inducer
Transcriptional repressor that recruits the Cyc8p-Tup1p complex to promoters;
mediates glucose repression and negatively regulates a variety of processes
including filamentous growth and alkaline pH response
Catalytic subunit of protein phosphatase; involved in activation of Gln3p, which
is a transcription factor with a role in nitrogen utilization
coordinates regulation of alpha-factor receptor signalling and induction of
morphogenesis during conjugation; cytoskeletal protein, similar to arrestins
Shared subunit of DNA polymerase epsilon and of ISW2/yCHRAC chromatin
accessibility complex; involved in both chromosomal DNA replication and in
inheritance of telomeric silencing
Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA
polymerase II transcription initiation and in chromatin modification, similar to
histone H2A
RNA-binding protein involved in the cleavage step of mRNA 3'-end formation
prior to polyadenylation; also involved in snoRNA maturation
involved in sterol uptake; zinc finger transcription factor of the Zn(2)-Cys(6)
binuclear cluster domain type
Positive transcriptional regulator, controls the expression of ADH2, peroxisomal
protein genes, and genes required for ethanol, glycerol, and fatty acid utilization
Protein of unknown function, potentially phosphorylated by Cdc28p
One of two nearly identical (see HTB2) histone H2B subtypes required for
chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated
ubiquitination regulates transcriptional activation, meiotic DSB formation and H3
methylation
One of two nearly identical (see also HTA2) histone H2A subtypes; core histone
required for chromatin assembly and chromosome function; DNA damage-
YDR247W
VHS1
YDR259C
YAP6
YDR264C
AKR1
YDR277C
MTH1
YDR283C
GCN2
YDR284C
DPP1
YDR296W
MHR1
YDR392W
SPT3
YDR423C
CAD1
YDR443C
SSN2
YDR451C
YHP1
YDR461W
YDR496C
MFA1
PUF6
YDR523C
SPS1
YDR527W
RBA50
YER028C
MIG3
YER040W
GLN3
YER045C
ACA1
YER054C
GIP2
dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by
Nat4p
Gene whose overexpression suppresses the synthetic lethality of the hal3 sit4
double mutation
Basic leucine zipper (bZIP) transcription factor
Negative regulator of pheromone response pathway; required for endocytosis of
pheromone receptors; involved in cell shape control; Ankyrin repeat-containing
protein
Negative regulator of the glucose-sensing signal transduction pathway, required
for repression of transcription by Rgt1p; interacts with Rgt1p and the Snf3p and
Rgt2p glucose sensors; phosphorylated by Yck1p, triggering Mth1p degradation
Protein kinase, phosphorylates the alpha-subunit of translation initiation factor
eIF2 (Sui2p) in response to starvation; activated by uncharged tRNAs and the
Gcn1p-Gcn20p complex
Diacylglycerol pyrophosphate (DGPP) phosphatase, zinc-regulated vacuolar
membrane-associated lipid phosphatase, dephosphorylates DGPP to
phosphatidate (PA) and Pi, then PA to diacylglycerol; involved in lipid signaling
and cell metabolism
Protein involved in mitochondrial homologous DNA recombination and in
transcription regulation; binds to activation domains of acidic activators;
presence in RNA pol II holoenzyme may help recruit an Ssn3p-active form of the
holoenzyme to target promoters
Subunit of the SAGA and SAGA-like transcriptional regulatory complexes,
interacts with Spt15p to activate transcription of some RNA polymerase IIdependent genes, also functions to inhibit trancription at some promoters
Transcriptional activator involved in resistance to 1,10-phenanthroline; member
of yeast Jun-family of transcription factors related to mammalian c-jun; basic
leucine zipper transcription factor
Required for stable association of Srb10p-Srb11p kinase with RNA polymerase
holoenzyme; regulates YGP1 epxression; component of RNA polymerase II
holoenzyme and Kornberg's mediator (SRB) subcomplex; transcription factor
acts as a repressor at early cell cycle boxes (ECBs) to restrict their activity to the
M/G1 phase of the cell cycle.
a-factor mating pheromone precursor
member of the PUF protein family; YDR496C
dispensable for mitosis, involved in middle/late stage of meiosis, required for
spore wall formation; serine/threonine kinase homologous to Ste20p; expressed
in middle/late meiosis
Protein required for cell viability
Probable transcriptional repressor involved in response to toxic agents such as
hydroxyurea that inhibit ribonucleotide reductase; phosphorylation by Snf1p or
the Mec1p pathway inactivates Mig3p, allowing induction of damage response
genes
Transcriptional activator of genes regulated by nitrogen catabolite repression
(NCR), localization and activity regulated by quality of nitrogen source
Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, may
regulate transcription of genes involved in utilization of non-optimal carbon
sources
Putative regulatory subunit of the protein phosphatase Glc7p, proposed to be
involved in glycogen metabolism; contains a conserved motif (GVNK motif) that
is also found in Gac1p, Pig1p, and Pig2p
YER069W
ARG5,6
YER088C
DOT6
YER161C
SPT2
YER177W
BMH1
YER184C
YER18
4C
YFL021W
GAT1
YFL026W
YFL028C
STE2
CAF16
YFL031W
HAC1
YFL033C
RIM15
YFL052W
YFL052
W
YFR009W
GCN20
YFR034C
PHO4
YGL014W
PUF4
YGL035C
MIG1
YGL037C
PNC1
YGL071W
RCS1
YGL073W
YGL096W
HSF1
MF(AL
PHA)2
TOS8
YGL099W
LSG1
YGL121C
GPG1
YGL158W
YGL162W
RCK1
SUT1
YGL166W
CUP2
YGL089C
Bifunctional enzyme with N-acetyl-gamma-glutamyl-phosphate reductase and
acetylglutamate kinase activities, catalyzes the second and third steps in the
biosynthesis of the arginine precursor ornithine; forms a complex with Arg2p
Protein of unknown function, involved in telomeric gene silencing and
filamentation
Protein involved in negative regulation of transcription, exhibits regulated
interactions with both histones and SWI-SNF components, has similarity to
mammalian HMG1 proteins
14-3-3 protein, major isoform; binds proteins and DNA, involved in regulation of
many processes including exocytosis and vesicle transport, Ras/MAPK signaling
during pseudohyphal development, rapamycin-sentitive signaling, and others
YER184C
Transcriptional activator of genes involved in nitrogen catabolite repression,
member of the GATA family of DNA binding proteins; activity and localization
regulated by nitrogen limitation and Ure2p
alpha-factor pheromone receptor; seven-transmembrane domain protein
CCR4 associated factor; ABC ATPase
bZIP transcription factor (ATF/CREB1 homolog) that regulates the unfoldedprotein response, via UPRE binding, and membrane biogenesis; ER stressinduced splicing pathway utilizing Ire1p, Trl1p and Ada5p facilitates efficient
Hac1p synthesis
RIM15 is glucose-repressed; RIM15 is required for IME2 expression; Trehaloseassociated protein kinase related to S. pombe cek1+
Positive regulator of the Gcn2p kinase activity, forms a complex with Gcn1p;
proposed to stimulate Gcn2p activation by an uncharged tRNA
Basic helix-loop-helix (bHLH) transcription factor; binds cooperatively with
Pho2p to the PHO5 promoter; function is regulated by phosphorylation at
multiple sites and by phosphate availability
member of the PUF protein family; YGL014W
Transcription factor involved in glucose repression; C2H2 zinc finger protein
which resembles the mammalian Egr and Wilms tumour proteins
NAD(+) salvage pathway gene; pyrazinamidase and nicotinamidase
Transcription factor that binds the consensus site PyPuCACCCPu, involved in
iron homeostasis and cell size regulation; activates the expression of target genes
in response to low-iron conditions
heat shock transcription factor
alpha mating factor
Target of SBF
Putative GTPase involved in 60S ribosomal subunit biogenesis; localized to the
cytoplasm
Proposed gamma subunit of the heterotrimeric G protein that interacts with the
receptor Grp1p; involved in regulation of pseudohyphal growth; requires Gpb1p
or Gpb2p to interact with Gpa2p
Serine/threonine protein kinase
Involved in sterol uptake; hypoxic gene family involved in sterol transport
Copper-binding transcription factor; activates transcription of the metallothionein
genes CUP1-1 and CUP1-2 in response to elevated copper concentrations
YGL178W
MPT5
YGL179C
TOS3
YGL180W
ATG1
YGL194C
HOS2
YGL195W
GCN1
YGL208W
SIP2
YGL209W
MIG2
YGL229C
SAP4
YGL248W
PDE1
YGL254W
FZF1
YGR014W
MSB2
YGR023W
MTL1
YGR040W
KSS1
YGR044C
RME1
YGR070W
ROM1
YGR097W
ASK10
YGR108W
YGR109C
CLB1
CLB6
YGR123C
PPT1
YGR152C
RSR1
YGR156W
YGR161C
PTI1
RTS3
YGR188C
BUB1
Protein that specifically binds to mRNAs encoding chromatin modifiers and
spindle pole body components; has roles in longevity, in maintenance of cell wall
integrity, and in sensitivity to and recovery from pheromone arrest
Putative protein kinase, related to and redundant with Elm1p and Pak1p in
activating the SNF1 complex
Protein serine/threonine kinase, required for autophagy and for the cytoplasm-tovacuole targeting (Cvt) pathway
Histone deacetylase required for gene activation via specific deacetylation of
lysines in H3 and H4 histone tails; subunit of the Set3 complex, a meioticspecific repressor of sporulation specific genes that contains deacetylase activity
Positive regulator of the Gcn2p kinase activity, forms a complex with Gcn20p;
proposed to stimulate Gcn2p activation by an uncharged tRNA
Member of a family of proteins, including Sip1p and Gal83p, that interact with
Snf1p and Snf4p and are involved in the response to glucose starvation;
component of Snf1 protein complex involved in response to glucose starvation
Involved in repression, along with Mig1p, of SUC2 (invertase) expression by
high levels of glucose; binds to Mig1p-binding sites in SUC2 promoter; Protein
containing zinc fingers very similar to zinc fingers in Mig1p
Protein required for function of the Sit4p protein phosphatase, member of a
family of similar proteins that form complexes with Sit4p, including Sap155p,
Sap185p, and Sap190p
Low-affinity cyclic AMP phosphodiesterase, controls glucose and intracellular
acidification-induced cAMP signaling, target of the cAMP-protein kinase A
(PKA) pathway; glucose induces transcription and inhibits translation
Transcription factor involved in sulfite resistance; contains five zinc-fingers;
activates SSU1 transcription
Protein that functions as an osmosensor in parallel to the Sho1p-mediated
pathway, multicopy suppressor of a temperature-sensitive mutation in CDC24,
potential Cdc28p substrate
Mid-Two Like 1; acts in concert with Mid2p to transduce cell wall stress signals
Mitogen-activated protein kinase (MAPK) involved in signal transduction
pathways that control filamentous growth and pheromone response
mediates cell type control of sporulation; negatively regulates IME1 and
sporulation; zinc finger protein; negative regulator of meiosis; directly repressed
by a1-a2 regulator
GDP/GTP exchange protein (GEP) for Rho1p; mutations are synthetically lethal
with mutations in rom2, which also encodes a GEP
Component of the RNA polymerase II holoenzyme, phosphorylated in response
to oxidative stress; has a role in destruction of Ssn8p, which relieves repression
of stress-response genes
Involved in mitotic induction; G(sub)2-specific B-type cyclin
role in DNA replication during S phase; B-type cyclin
Protein serine/threonine phosphatase with similarity to human phosphatase PP5;
present in both the nucleus and cytoplasm; expressed during logarithmic growth
Gtp-binding protein of the ras superfamily involved in bud site selection; GTPbinding protein, ras superfamily
Pta1p Interacting protein
Hypothetical ORF
checkpoint gene involved in permitting entry into mitosis depending upon the
assembly state of microtubules; Serine/threonine protein kinase required for cell
cycle arrest in response to loss of microtubule function
YGR200C
ELP2
YGR203W
YGR20
3W
YGR233C
PHO81
YGR249W
MGA1
YGR288W
MAL13
YHL009C
YAP3
YHL027W
RIM101
YHL028W
WSC4
YHR005C
GPA1
YHR006W
STP2
YHR030C
YHR041C
YHR056C
SLT2
SRB2
RSC30
YHR084W
STE12
YHR099W
TRA1
YHR122W
YHR12
2W
YHR136C
SPL2
YHR178W
STB5
YIL033C
BCY1
YIL050W
PCL7
YIL101C
XBP1
YIL119C
RPI1
Elongator protein, part of the six-subunit RNA polymerase II Elongator histone
acetyltransferase complex; target of Kluyveromyces lactis zymocin
Cyclin-dependent kinase (CDK) inhibitor, regulates Pho80p-Pho85p and Pcl7pPho85p cyclin-CDK complexes in response to phosphate levels; required for
derepression of PHO5; transcriptionally regulated by Pho4p and Pho2p
Mga1p shows similarity to heat shock transcription factor
MAL-activator protein, part of complex locus MAL1; nonfunctional in genomic
reference strain S288C
bZIP transcription factor
Transcriptional activator required for entry into meiosis, has similarity to the
Aspergillus Phenotype-response regulator PacC and the Yarrowia proteinase
YlRim1010p; Meiotic regulatory protein; Cys-His zinc fingers
cell wall integrity and stress response component 4; Putative integral membrane
protein containing novel cysteine motif. Similarity to SLG1 (WSC1), WSC2 and
WSC3
Alpha subunit of G protein coupled to mating factor receptors, involved in the
mating pheromone signal transduction pathway; component of pheromone
response pathway common to both a and alpha cells
Transcription factor, activated by proteolytic processing in response to signals
from the SPS sensor system for external amino acids; activates transcription of
amino acid permease genes
Suppressor of lyt2; serine/threonine MAP kinase
RNA polymerase II holoenzyme/mediator subunit
RSC complex component
Transcription factor that is activated by a MAP kinase signaling cascade,
activates genes involved in mating or pseudohyphal/invasive growth pathways;
cooperates with Tec1p transcription factor to regulate genes specific for invasive
growth
Histone acetyltransferase component, putative ortholog of human TRRAP which
is an essential cofactor of c-Myc
Protein with similarity to cyclin-dependent kinase inhibitors, overproduction
suppresses a plc1 null mutation; green fluorescent protein (GFP)-fusion protein
localizes to the cytoplasm in a punctate pattern
binds Sin3p in two-hybrid assay; Zinc finger (6-Cys)
Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA), a
component of a signaling pathway that controls a variety of cellular processes,
including metabolism, cell cycle, stress response, stationary phase, and
sporulation
Pho85p cyclin of the Pho80p subfamily, forms a functional kinase complex with
Pho85p which phosphorylates Mmr1p and is regulated by Pho81p; involved in
glycogen metabolism, expression is cell-cycle regulated
Transcriptional repressor that binds to promoter sequences of the cyclin genes,
CYS3, and SMF2; expression is induced by stress or starvation during mitosis,
and late in meiosis; member of the Swi4p/Mbp1p family; potential Cdc28p
substrate
Putative transcriptional regulator; overexpression suppresses the heat shock
sensitivity of wild-type RAS2 overexpression and also suppresses the cell lysis
defect of an mpk1 mutation
YIL130W
YIL130
W
YIL131C
FKH1
YIL147C
SLN1
YIL153W
RRD1
YIL154C
IMP2'
YIR017C
MET28
YIR018W
YIR026C
YAP5
YVH1
YIR033W
MGA2
YJL005W
CYR1
YJL056C
ZAP1
YJL065C
DLS1
YJL089W
SIP4
YJL098W
SAP185
YJL103C
YJL103
C
YJL127C
SPT10
YJL128C
PBS2
YJL141C
YAK1
YJL157C
FAR1
YJL164C
TPK1
YJL187C
SWE1
YJR053W
BFA1
YJR060W
CBF1
YIL130W
Transcription factor of the forkhead family that regulates the cell cycle and
pseudohyphal growth; also involved in chromatin silencing at HML and HMR
Histidine kinase osmosensor that regulates a MAP kinase cascade;
transmembrane protein with an intracellular kinase domain that signals to Ypd1p
and Ssk1p, thereby forming a phosphorelay system similar to bacterial twocomponent regulators
Resistant to Rapamycin Deletion
Transcriptional activator involved in maintenance of ion homeostasis and
protection against DNA damage caused by bleomycin and other oxidants,
contains a C-terminal leucine-rich repeat
Transcriptional activator in the Cbf1p-Met4p-Met28p complex, participates in
the regulation of sulfur metabolism
nitrogen starvation-induced protein phosphatase
ER membrane protein involved, with its homolog Spt23p, in regulation of OLE1
transcription; inactive ER form dimerizes and one subunit is then activated by
ubiquitin/proteasome-dependent processing followed by nuclear targeting
Required for START A of cell cycle, and glucose and nitrogen repression of
sporulation; adenylate cyclase
Zinc-regulated transcription factor, binds to zinc-responsive promoter elements to
induce transcription of certain genes in the presence of zinc; regulates its own
transcription; contains seven zinc-finger domains
Subunit of ISW2/yCHRAC chromatin accessibility complex along with Itc1p,
Isw2p, and Dpb4p; involved in inheritance of telomeric silencing
Possibly involved in Snf1p regulated transcriptional activation; shows homology
to DNA binding domain of Gal4p, has a leucine zipper motif and acidic region;
lexA-Sip4p activates transcription
Protein that forms a complex with the Sit4p protein phosphatase and is required
for its function; member of a family of similar proteins including Sap4p,
Sap155p, and Sap190p
YJL103C
Putative histone acetylase, required for transcriptional regulation at core
promoters, functions at or near the TATA box
MAP kinase kinase that plays a pivotal role in the osmosensing signaltransduction pathway, activated under severe osmotic stress
Serine-threonine protein kinase
Cyclin-dependent kinase inhibitor that mediates cell cycle arrest in response to
pheromone; also forms a complex with Cdc24p, Ste4p, and Ste18p that may
specify the direction of polarized growth during mating; potential Cdc28p
substrate
putative catalytic subunit of cAMP-dependent protein kinase
Protein kinase that regulates the G2/M transition by inhibition of Cdc28p kinase
activity; localizes to the nucleus and to the daughter side of the mother-bud neck;
homolog of S. pombe Wee1p; potential Cdc28p substrate
Component of the GTPase-activating Bfa1p-Bub2p complex involved in multiple
cell cycle checkpoint pathways that control exit from mitosis
Helix-loop-helix protein that binds the motif CACRTG (R=A or G), which is
YJR094C
IME1
YJR122W
CAF17
YJR122W
CAF17
YJR127C
ZMS1
YJR147W
HMS2
YKL032C
IXR1
YKL043W
PHD1
YKL062W
MSN4
YKL101W
HSL1
YKL109W
HAP4
YKL126W
YPK1
YKL161C
YKL16
1C
YKL178C
STE3
YKL189W
HYM1
YKL198C
PTK1
YKR019C
IRS4
YKR099W
BAS1
YLL010C
PSR1
present at several sites including MET gene promoters and centromere DNA
element I (CDEI); required for nucleosome positioning at this motif; targets
Isw1p to DNA
Master regulator of meiosis that is active only during meiotic events, activates
transcription of early meiotic genes through interaction with Ume6p, degraded by
the 26S proteasome following phosphorylation by Ime2p
Mitochondrial protein that interacts with Ccr4p in the two-hybrid system; 3'untranslated region contains a putative mRNA localization element common to
genes encoding mitochondrial proteins
Mitochondrial protein that interacts with Ccr4p in the two-hybrid system; 3'untranslated region contains a putative mRNA localization element common to
genes encoding mitochondrial proteins
Zinc-finger protein that localizes to the nucleus, putative transcriptional regulator
of ALD6
Protein with similarity to heat shock transcription factors; overexpression
suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2
homozygous null mutant
Protein that binds DNA containing intrastrand cross-links formed by cisplatin,
contains two HMG (high mobility group box) domains, which confer the ability
to bend cisplatin-modified DNA; mediates aerobic transcriptional repression of
COX5b
protein similar to StuA of Aspergillus nidulans; putative transcription factor
Transcriptional activator related to Msn2p; activated in stress conditions, which
results in translocation from the cytoplasm to the nucleus; binds DNA at stress
response elements of responsive genes, inducing gene expression
Nim1p-related protein kinase that regulates the morphogenesis and septin
checkpoints; associates with the assembled septin filament; required along with
Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p
Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAATbinding complex, a transcriptional activator and global regulator of respiratory
gene expression; provides the principal activation function of the complex
76.5 kDa Serine/threonine protein kinase with similarity to protein kinase C, is
90% identical to Ypk2p
YKL161C
Cell surface a factor receptor, transcribed in alpha cells and required for mating
by alpha cells, couples to a MAP kinase cascade to mediate pheromone response;
ligand bound receptors undergo endocytosis and recyling to the plasma
membrane
Component of the RAM signaling network that is involved in regulation of
Ace2p activity and cellular morphogenesis, interacts with Kic1p and Sog2p,
localizes to sites of polarized growth during budding and during the mating
response
Putative serine/threonine protein kinase; probable serine/threonine-specific
protein kinase (EC 2.7.1.-)
Protein involved in regulation of phosphatidylinositol 4,5-bisphosphate
concentrations; Irs4p and Tax4p bind and activate the phosphatase Inp51p;
mutation confers an increase in rDNA silencing
Myb-related transcription factor involved in regulating basal and induced
expression of genes of the purine and histidine biosynthesis pathways
Plasma membrane associated protein phosphatase involved in the general stress
response; required along with binding partner Whi2p for full activation of STREmediated gene expression, possibly through dephosphorylation of Msn2p
YLL016W
YLL01
6W
YLL016W
YLL019C
KNS1
Nonessential putative protein kinase of unknown cellular role; member of the
LAMMER family of protein kinases, which are serine/threonine kinases also
capable of phosphorylating tyrosine residues
YLL054C
YLL05
4C
YLL054C
YLR150W
STM1
YLR183C
TOS4
YLR256W
HAP1
YLR332W
MID2
YLR336C
SGD1
YLR452C
SST2
YML016C
PPZ1
YML027W
YOX1
YMR001C
CDC5
YMR016C
SOK2
YMR019W
STB4
YMR030W
RSF1
YMR036C
MIH1
YMR042W
ARG80
YMR053C
STB2
YMR136W
GAT2
YMR179W
SPT21
YMR199W
CLN1
YMR228W
MTF1
Protein that binds quadruplex nucleic acids; multicopy suppressor of tom1 and
pop2 mutations; acts with Cdc13p to maintain telomere structure
Transcription factor that binds to a number of promoter regions, particularly
promoters of some genes involved in pheromone response and cell cycle;
potential Cdc28p substrate; expression is induced in G1 by bound SBF
Heme-responsive zinc finger transcription factor of the Zn(2)-Cys(6) binuclear
cluster domain type; redox sensing regulator of gene expression (activates CYC1,
CYC7, CYP3, CYB2, CTT1, COR2, ROX1, ERG9, ERG11, SOD2 and YHB1;
represses HEM13)
Protein required for mating
Suppressor of Glycerol Defect; may be involved in high osmolarity signaling
pathway
Protein involved in desensitization to alpha-factor pheromone; member of the
RGS (regulator of G-protein signalling) family; GTPase-activating protein
Serine/threonine protein phosphatase Z, isoform of Ppz2p; involved in regulation
of potassium transport, which affects osmotic stability, cell cycle progression,
and halotolerance
Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early
cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed
in M/G1 phase; expression is cell cycle-regulated; potential Cdc28p substrate
Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at
bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis
through phosphorylation of substrates; may be a Cdc28p substrate
Protein that can when overexpressed suppress mutants of cAMP-dependent
protein kinase; displays homologies to several transcription factors
Protein that binds Sin3p in a two-hybrid assay
Protein localized to both the nucleus and mitochondrion; mutant displays
decreased transcription of specific nuclear and mitochondrial genes whose
products are involved in respiratory growth
S. pombe cdc25+ homolog; homolog of S. pombe cdc25
Regulator of arginine-responsive genes with ARG81 and ARG82; transcription
factor
Protein that binds Sin3p in a two-hybrid assay and is part of a large protein
complex with Sin3p and Stb1p
Protein containing GATA family zinc finger motifs; similar to Gln3p and
Dal80p; expression repressed by leucine
Protein required for normal transcription at several loci including HTA2-HTB2
and HHF2-HHT2, but not required at the other histone loci; functionally related
to Spt10p
role in cell cycle START; G(sub)1 cyclin
Mitochondrial RNA polymerase sigma-like specificity factor required for
promoter recognition, interacts with mitochondrial core polymerase Rpo41p,
YMR280C
CAT8
YNL023C
FAP1
YNL030W
HHF2
YNL031C
HHT2
YNL068C
FKH2
YNL088W
TOP2
YNL103W
MET4
YNL136W
YNL145W
EAF7
MFA2
YNL173C
MDG1
YNL180C
RHO5
YNL229C
URE2
YNL239W
LAP3
YNL255C
GIS2
YNL262W
POL2
YNL289W
PCL1
YOL016C
YNL30
5C
ESF2
YNR06
3W
CMK2
YOL051W
GAL11
YOL100W
YOL113W
PKH2
SKM1
YNL305C
YNR054C
YNR063W
imported into mitochondria via a novel process requiring most of the Mtf1p
sequence
Zinc-cluster protein involved in activating gluconeogenic genes; related to Gal4p
Protein that binds to Fpr1p (FKBP12), conferring rapamycin resistance by
competing with rapamycin for Fpr1p binding; has similarity to putative
transcription factors, including D. melanogaster shuttle craft and human NFX1
One of two identical histone H4 proteins (see also HHF1); core histone required
for chromatin assembly and chromosome function; contributes to telomeric
silencing; N-terminal domain involved in maintaining genomic integrity
One of two identical histone H3 proteins (see also HHT1); core histone required
for chromatin assembly, involved in heterochromatin-mediated telomeric and
HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation
Transcription factor of the forkhead family that regulates the cell cycle and
pseudohyphal growth; also involved in chromatin silencing at HML and HMR;
Essential type II topoisomerase, catalyzes topology changes in DNA via transient
breakage and rejoining of phosphodiester bonds in the DNA backbone; localizes
to axial cores in meiosis
Lecine-zipper transcriptional activator, responsible for the regulation of the sulfur
amino acid pathway, requires different combinations of the auxiliary factors
Cbf1p, Met28p, Met31p and Met32p
Subunit of the NuA4 histone acetyltransferase complex
lipopeptide mating pheromone; mating a-factor pheromone precursor
Plasma membrane protein involved in G-protein mediated pheromone signaling
pathway; overproduction suppresses bem1 mutations
Non-essential small GTPase of the Rho/Rac subfamily of Ras-like proteins,
likely involved in protein kinase C (Pkc1p)-dependent signal transduction
pathway that controls cell integrity
Nitrogen catabolite repression regulator that acts by inhibition of GLN3
transcription in good nitrogen source; altered form of Ure2p creates [URE3]
prion
Aminopeptidase of cysteine protease family, has a DNA binding activity and acts
as bleomycin hydrolase in vitro; transcription is regulated by galactose via Gal4p
Putative zinc finger protein with similarity to human CNBP, proposed to be
involved in the RAS/cAMP signaling pathway
Catalytic subunit of DNA polymerase epsilon, one of the major chromosomal
DNA replication polymerases characterized by processivity and proofreading
exonuclease activity; also involved in DNA synthesis during DNA repair
Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell
cycle and regulation of morphogenesis, localizes to sites of polarized cell growth
Calmodulin-dependent protein kinase
Component of the Mediator complex; interacts with RNA polymerase II and the
general transcription factors to form the RNA polymerase II holoenzyme; affects
transcription by acting as target of activators and repressors
Pkb-activating Kinase Homologue; Ser/Thr protein kinase
Serine/threonine protein kinase with similarity to Ste20p and Cla4p
YOL133W
HRT1
YOR028C
CIN5
YOR032C
HMS1
YOR047C
STD1
YOR083W
WHI5
YOR090C
YOR101W
PTC5
RAS1
YOR107W
RGS2
YOR125C
CAT5
YOR162C
YRR1
YOR178C
GAC1
YOR210W
YOR213C
YOR224C
YOR229W
YOR230W
RPB10
SAS5
RPB8
WTM2
WTM1
YOR304W
ISW2
YOR337W
TEA1
YOR344C
TYE7
YOR363C
PIP2
YPL002C
SNF8
YPL016W
SWI1
YPL026C
SKS1
RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases
(SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether
Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of
SCF
Basic leucine zipper transcriptional factor of the yAP-1 family that mediates
pleiotropic drug resistance and salt tolerance; localizes constitutively to the
nucleus
C2H2 zinc-finger protein with similarity to myc-family transcription factors;
overexpression confers hyperfilamentous growth and suppresses the
pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null
mutant
Protein that interacts with the Snf1p protein kinase and Spt15p in two-hybrid and
in in vitro binding studies
Protein that regulates the critical cell size required for passage through Start and
commitment to cell division; may act upstream of SCB binding factor (SBF) and
MCB binding factor (MBF); periodically expressed in G1
Phosphatase type Two C; Type 2C Protein Phosphatase
ras proto-oncogene homolog
Negative regulator of glucose-induced cAMP signaling; directly activates the
GTPase activity of the heterotrimeric G protein alpha subunit Gpa2p
may encode a protein involved in one or more monoxygenase or hydroxylase
steps of ubiquinone biosynthesis
Zn2-Cys6 zinc-finger transcription factor that activates genes involved in
multidrug resistance; paralog of Yrm1p, acting on an overlapping set of target
genes
Regulatory subunit for Glc7p (protein phosphatase I) for glycogen synthesis;
regulatory role also predicted for glucose repression and ion homeostatis;
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
Protein involved in silencing at telomeres, HML, and HMR
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
WD repeat containing transcriptional modulator 2; Transcriptional modulator
WD repeat containing transcriptional modulator 1; Transcriptional modulator
Member of the imitation-switch (ISWI) class of ATP-dependent chromatin
remodeling complexes; ATPase component that, with Itc1p, forms a complex
required for repression of a-specific genes, INO1, and early meiotic genes during
mitotic growth
Mutants are defective in Ty1 Enhancer-mediated Activation; Ty1 enhancer
activator
may be involved in glycolytic gene expression; TYE7, a 33 kDa serine-rich
protein, is a potential member of the basic region/helix-loop-helix/leucine-zipper
protein family
peroxisome induction pathway 2 (PIP2); transcriptional activator of peroxisome
proliferation; may form heterodimer with Oaf1 to activate oleate-inducible gene
expression; activator of peroxisome proliferation
appears to be functionally related to SNF7; involved in glucose derepression
Global transcription activator that acts in complex with Snf2p, Snf5p, Snf6p, and
Swi3p to assist gene-specific activators; involved in the regulation of expression
of many genes, including ADH1, ADH2, GAL1, HO, INO1 and SUC2; Zincfinger transcription factor
multicopy suppressor of snf3 and grr1 mutants; serine/threonine protein kinase
YPL046C
ELC1
YPL075W
GCR1
YPL086C
ELP3
YPL089C
RLM1
YPL127C
HHO1
YPL140C
MKK2
YPL153C
RAD53
YPL161C
BEM4
YPL177C
CUP9
YPL181W
CTI6
YPL187W
MF(AL
PHA)1
YPL203W
TPK2
YPL204W
HRR25
YPL256C
YPL230
W
CLN2
YPR005C
HAL1
YPR013C
YPR01
3C
YPL230W
YPR018W
RLF2
YPR030W
CSR2
homologous to Ran1p
Elongin C, forms heterodimer with Ela1p that participates in transcription
elongation; expression dramatically upregulated during sporulation; widely
conserved among eukaryotes
Transcriptional activator of genes involved in glycolysis, functions and interacts
with Gcr2p
Histone acetyltransferase subunit of the Elongator complex, which is a
component of the RNA polymerase II holoenzyme; activity is directed
specifically towards histones H3 and H4; disruption confers resistance to K.
lactis zymotoxin
serum response factor-like protein that may function downstream of MPK1
(SLT2) MAP-kinase pathway; serum response factor-like protein
Histone H1, a linker histone required for nucleosome packaging at restricted
sites; suppresses DNA repair involving homologous recombination; not required
for telomeric silencing, basal transcriptional repression, or efficient sporulation
Member of MAP kinase pathway involving PKC1, BCK1, and SLT2. Shows
functional redundancy with MKK1; protein kinase
Protein kinase, required for cell-cycle arrest in response to DNA damage;
activated
by
trans
autophosphorylation
when
interacting
with
hyperphosphorylated Rad9p
Protein involved in establishment of cell polarity and bud emergence; interacts
with the Rho1p small GTP-binding protein and with the Rho-type GTPase
Cdc42p
Homeodomain-containing transcriptional repressor of PTR2, which encodes a
major peptide transporter; imported peptides activate ubiquitin-dependent
proteolysis, resulting in degradation of Cup9p and de-repression of PTR2
transcription
Protein that relieves transcriptional repression by binding to the Cyc8p-Tup1p
corepressor and recruiting the SAGA complex to the repressed promoter;
contains a PHD finger domain
mating factor alpha
Involved in nutrient control of cell growth and division; cAMP-dependent protein
kinase catalytic subunit
Similar to YCK1 and YCK2, two other casein kinase I isoforms; found primarily
in nucleus; may be involved in DNA-damage repair; casein kinase I isoform
Cytoplasmic protein involved in halotolerance; decreases intracellular Na+ (via
Ena1p) and increases intracellular K+ by decreasing efflux; expression repressed
by Ssn6p-Tup1p and Sko1p and induced by NaCl, KCl, and sorbitol through
Gcn4p
Chromatin Assembly Complex, subunit 1: largest (p90) subunit of three-subunit
protein complex (yeast CAF-I) involved in DNA-replication-linked nucleosome
assembly. Homol. to p150 subunit human Chromatin Assembly Factor-I (CAF-I);
p90 subunit of yeast Chromatin Assembly Factor-I (CAF-I)
Nuclear protein with a potential regulatory role in utilization of galactose and
nonfermentable carbon sources; overproduction suppresses the lethality at high
YPR034W
ARP7
YPR052C
NHP6A
YPR054W
SMK1
YPR065W
ROX1
YPR070W
MED1
YPR106W
ISR1
YPR111W
DBF20
YPR179C
HDA3
YPR199C
ARR1
temperature of a chs5 spa2 double null mutation; potential Cdc28p substrate
involved in transcriptional regulation; actin related protein, subunit of the
chromatin remodeling Snf/Swi complex
Homologous to mammalian high mobility group proteins 1 and 2; functions
redundantly with the highly homologous gene, NHP6B; high-mobility group
non-histone chromatin protein; 11-kDa nonhistone chromosomal protein
Mitogen-activated protein kinase required for spore morphogenesis that is
expressed as a middle sporulation-specific gene
Heme-dependent repressor of hypoxic genes; contains an HMG domain that is
responsible for DNA bending activity
Subunit 1 of the Mediator complex essential for transcriptional regulation
Predicted protein kinase, overexpression causes sensitivity to staurosporine,
which is a potent inhibitor of protein kinase C
Ser/Thr kinase involved in late nuclear division, one of the mitotic exit network
(MEN) proteins; necessary for the execution of cytokinesis
Subunit of a possibly tetrameric trichostatin A-sensitive class II histone
deacetylase complex that contains an Hda1p homodimer and an Hda2p-Hda3p
heterodimer; required for the activity of the complex; has similarity to Hda2p
Transcriptional activator of the bZIP family, required for transcription of genes
involved in resistance to arsenic compounds
Table 2: 581 genotype regulators
We used the genotype values, measured in 2,957 genetic markers by Brem & Kruglyak. We
merged the adjacent markers with no more than 3 mismatches, resulted in 581 markers
listed below.
Genotype
regulators
Genomic region
Ch Start
End
r
M1_1_37068
1
1
37068
M1_41483_41483
1
41483
41483
M1_42255_42255
1
42255
42255
M1_42489_42489
1
42489
42489
M1_42591_42591
1
42591
42591
M1_42633_42633
1
42633
42633
M1_42639_42639
1
42639
42639
M1_51324_52943
1
51324
52943
M1_55215_55329
1
55215
55329
M1_74577_74577
1
74577
74577
M1_89879_94468
1
89879
94468
M1_133611_1336
11
1
133611
133611
M1_134580_1662
21
1
134580
166221
M1_184243_1872
72
1
184243
187272
Genes that are located within 10kb upstream/
downstream of the genomic region covered by the
genotype regulator
ACS1 PEX22 YAL056C-A GPB2 CNE1 YAL058C-A
YAL059C-A ECM1 BDH1 YAL061W GDH3 FLO9
YAL063C-A YAL064C-A YAL064W YAL064W-B
YAL065C YAL066W SEO1 YAL067W-A YAL068C
YAL068W-A YAL069W
OAF1 YAL053W ACS1 PEX22 YAL056C-A GPB2
CNE1 YAL058C-A YAL059C-A ECM1 BDH1
YAL061W GDH3
YAL049C OAF1 YAL053W ACS1 PEX22 YAL056C-A
GPB2 CNE1 YAL058C-A YAL059C-A ECM1 BDH1
YAL061W
YAL061W
YAL061W
YAL061W
YAL061W
YAL042C-A ERV46 PTA1 YAL043C-A GCV3
YAL044W-A YAL045C YAL046C SPC72 YAL047W-A
GEM1 YAL049C OAF1 YAL053W ACS1 PEX22
CDC24 YAL042C-A ERV46 PTA1 YAL043C-A GCV3
YAL044W-A YAL045C YAL046C SPC72 YAL047W-A
GEM1 YAL049C OAF1 YAL053W
PRP45 POP5 FUN19 YAL034C-B MTW1 FUN12 RBG1
YAL037C-A YAL037C-B YAL037W CDC19 CYC3
CLN3
LTE1 MAK16 DRS2 YAL026C-A YAL027W FRT2
MYO4 SNC1 FUN21 YAL031W-A PRP45 POP5 FUN19
MTW1
EFB1 YAL004W SSA1 ERP2 FUN14 SPO7 MDM10
SWC3 CYS3 DEP1 SYN8 NTG1 YAL016C-A
YAL016C-B TPD3
TFC3 VPS8 EFB1 YAL004W SSA1 ERP2 FUN14 SPO7
MDM10 SWC3 CYS3 DEP1 SYN8 NTG1 YAL016C-A
TPD3 ERP1 NUP60 SWD1 RFA1 SEN34 YAR009C
BUD14 ADE1 KIN3 CDC15 YAR019W-A
YAR019W-A PAU7 YAR023C UIP3 YAR028W
YAR029W YAR030C PRM9 MST28 YAR035C-A YAT1
M1_187402_1876
40
M1_192130_1932
51
M1_198261_2084
97
M1_229090_2291
40
1
187402
187640
1
192130
193251
1
198261
208497
1
229090
229140
M2_9425_36365
2
9425
36365
M2_50915_50915
2
50915
50915
M2_73342_76948
2
73342
76948
M2_87845_87845
2
87845
87845
M2_133737_1516
86
2
133737
151686
M2_162382_1656
92
2
162382
165692
M2_175071_1911
71
2
175071
191171
M2_197673_1991
07
2
197673
199107
M2_206323_2128
42
2
206323
212842
M2_216978_2461
35
2
216978
246135
2
252538
256896
2
301671
301671
2
310928
310928
M2_328489_3340
16
2
328489
334016
M2_334020_3340
22
2
334020
334022
M2_252538_2568
96
M2_301671_3016
71
M2_310928_3109
28
SWH1 YAR044W
YAR023C UIP3 YAR028W YAR029W YAR030C PRM9
MST28 YAR035C-A YAT1 SWH1 YAR044W
UIP3 YAR028W YAR029W YAR030C PRM9 MST28
YAR035C-A YAT1 SWH1 YAR044W YAR047C
MST28 YAR035C-A YAT1 SWH1 YAR044W YAR047C
FLO1 YAR053W YAR060C YAR061W
YAR064W YAR066W YAR068W YAR069C YAR070C
PHO11 IMD1 YAR075W
RPL32 ROX3 YBL094C YBL095W YBL096C BRN1
BNA4 ATP1 YBL100C ECM21 YBL101W-A
YBL101W-B YBL101W-C SFT2 RTG3 YBL103C-A
YBL104C PKC1 SRO77 YBL107C YBL107W-A
YBL108C-A YBL108W YBL109W YBL111C YBL112C
YBL113C YBL113W-A
RPL23A TEL1 AVT5 MRP21 MAP2 SCS22 RPL32
ROX3 YBL094C YBL095W YBL096C BRN1
SSA3 ILS1 YBL077W ATG8 NUP170 PET112
YBL081W RHK1 YBL083C CDC27 BOI1
UBP13 PRS4 YBL068W-A AST1 YBL070C YBL071C
YBL071C-B KTI11 RPS8A YBL073W AAR2 SSA3 ILS1
YBL077W ATG8
HEK2 RIB1 STU1 POL12 YBL036C APL3 MRPL16
URA7 YBL039C-A YBL039W-A ERD2 PRE7 FUI1
ECM13 YBL044W COR1 YBL046W EDE1 YBL048W
MOH1 SEC17 PIN4
NCL1 RRN10 LSM2 RPL19B YBL028C YBL029C-A
YBL029W PET9 SHE1 HEK2 RIB1 STU1 POL12
RRN6 ACH1 FUS3 PEP1 POP8 APN2 RFT1 HAP3 PIM1
MCM2 NCL1 RRN10 LSM2 RPL19B YBL028C
YBL029W
YBL009W YBL010C SCT1 YBL012C FMT1 RRN6
ACH1 FUS3 PEP1
PDR3 YBL005W-A LDB7 YBL006W-A SLA1 HIR1
YBL008W-A YBL009W YBL010C SCT1 YBL012C
FMT1 RRN6
ECM15 HTB2 HTA2 UTP20 PDR3 YBL005W-A
YBL005W-B LDB7 YBL006W-A SLA1 HIR1
YBL008W-A YBL009W NTH2 RER2 COQ1 GPI18
RCR1 UGA2 DSF2 FLR1 HHF1
COQ1 GPI18 RCR1 UGA2 DSF2 FLR1 HHF1 HHT1
IPP1 YBR012C YBR012W-B YBR013C
ETR1 YBR027C YBR028C CDS1 YBR030W RPL4A
YBR032W EDS1 HMT1 PDX3 CSG2 SCO1
YBR032W EDS1 HMT1 PDX3 CSG2 SCO1 CHS2 ATP3
FIG1 FAT1
FAT1 YBR042C QDR3 TCM62 GIP1 ZTA1 FMP23
RPS11B REB1 REG2 YBR051W YBR052C YBR053C
YRO2
TCM62 GIP1 ZTA1 FMP23 RPS11B REB1 REG2
YBR051W YBR052C YBR053C YRO2
M2_343931_3439
31
2
343931
343931
M2_352257_3680
60
2
352257
368060
M2_368991_3768
72
2
368991
376872
M2_380926_3888
62
2
380926
388862
M2_391856_4015
68
2
391856
401568
M2_406888_4205
28
2
406888
420528
M2_424450_4276
83
2
424450
427683
M2_477206_4866
40
2
477206
486640
M2_489202_4892
02
2
489202
489202
M2_499012_5134
08
2
499012
513408
M2_514035_5304
81
2
514035
530481
M2_533262_5557
87
2
533262
555787
M2_562409_5702
29
2
562409
570229
M2_573491_6037
90
2
573491
603790
M2_608310_6282
24
2
608310
628224
M2_636332_6424
2
636332
642453
REB1 REG2 YBR051W YBR052C YBR053C YRO2
PRP6 YBR056W YBR056W-A MUM2
YRO2 PRP6 YBR056W YBR056W-A MUM2 UBP14
TSC3 AKL1 ORC2 TRM7 YBR062C YBR063C
YBR064W ECM2 NRG2 TIP1 BAP2 TAT1
ORC2 TRM7 YBR062C YBR063C YBR064W ECM2
NRG2 TIP1 BAP2 TAT1 YBR070C YBR071W
YBR072C-A HSP26 RDH54
TIP1 BAP2 TAT1 YBR070C YBR071W YBR072C-A
HSP26 RDH54 YBR074W YBR075W YBR076C-A
ECM8 EGO3 ECM33 RPG1
YBR072C-A HSP26 RDH54 YBR074W YBR075W
YBR076C-A ECM8 EGO3 ECM33 RPG1 SEC18 SPT7
UBC4 TEC1
SEC18 SPT7 UBC4 TEC1 RPL19A MIS1 YBR085C-A
AAC3 IST2 RFC5 POL30 NHP6B YBR089W YBR090C
YBR090C-A MRS5 PHO3 PHO5
RPL19A YBR085C-A AAC3 IST2 RFC5 POL30 NHP6B
YBR089W YBR090C YBR090C-A MRS5 PHO3 PHO5
YBR094W RXT2 YBR096W
RAD16 LYS2 YBR116C TKL2 TEF2 MUD1 CBP6
GRS1 YBR121C-A MRPL36 TFC1 YBR124W PTC4
TPS1 YBR126W-A YBR126W-B VMA2 ATG14 OPY1
SHE3
MUD1 CBP6 GRS1 YBR121C-A MRPL36 TFC1
YBR124W PTC4 TPS1 YBR126W-A YBR126W-B
VMA2 ATG14 OPY1 SHE3 YBR131C-A CCZ1
TPS1 YBR126W-A YBR126W-B VMA2 ATG14 OPY1
SHE3 YBR131C-A CCZ1 AGP2 HSL7 YBR134W CKS1
MEC1 YBR137W YBR138C YBR139W IRA1
YBR134W CKS1 MEC1 YBR137W YBR138C
YBR139W IRA1 YBR141C YBR141W-A MAK5 SUP45
YBR144C ADH5 MRPS9 YBR147W YSW1
YBR141C YBR141W-A MAK5 SUP45 YBR144C ADH5
MRPS9 YBR147W YSW1 ARA1 TBS1 APD1 SPP381
RIB7 RPB5 CNS1 SLI15 ICS2 AMN1 YBR159W CDC28
CSH1 TOS1 YSY6
ICS2 AMN1 YBR159W CDC28 CSH1 TOS1 YSY6
DEM1 ARL1 UBS1 TYR1 POP7 PEX32 SSE2 NPL4
SEC66
TOS1 YSY6 DEM1 ARL1 UBS1 TYR1 POP7 PEX32
SSE2 NPL4 SEC66 SMY2 UMP1 YBR174C SWD3
ECM31 EHT1 YBR178W FZO1 DTR1 RPS6B SMP1
YBR182C-A YPC1 YBR184W MBA1 PCH2 YBR187W
NTC20 RPS9B YBR190W RPL21A YBR191W-A RIM2
MED8 SOY1 MSI1 PGI1
MBA1 PCH2 YBR187W NTC20 RPS9B YBR190W
RPL21A YBR191W-A RIM2 MED8 SOY1 MSI1 PGI1
YBR196C-A YBR196C-B YBR197C TAF5 KTR4 BEM1
YBR200W-A DER1 CDC47 COS111 YBR204C KTR3
YBR206W FTH1
CDC47 COS111 YBR204C KTR3 YBR206W FTH1
53
M2_658746_6587
46
2
658746
658746
M2_667083_6813
61
2
667083
681361
M2_681442_6978
94
2
681442
697894
M2_716885_7168
85
2
716885
716885
M2_732086_7320
92
2
732086
732092
M2_737531_7398
49
2
737531
739849
M2_745748_7540
59
2
745748
754059
M2_760429_7731
56
2
760429
773156
M3_14066_14066
3
14066
14066
M3_43867_43879
3
43867
43879
M3_54436_54436
3
54436
54436
M3_64311_64311
3
64311
64311
M3_75021_76127
3
75021
76127
M3_79091_92391
3
79091
92391
M3_100213_1050
42
3
100213
105042
M3_175799_2011
67
3
175799
201167
DUR1,2 YBR209W ERV15 AME1 NGR1 MET8 SDS24
NGR1 MET8 SDS24 HPC2 YBP1 ATG12 PYC2
YBR219C YBR220C PDB1 YBR221W-A PCS60
ATG12 PYC2 YBR219C YBR220C PDB1 YBR221W-A
PCS60 TDP1 YBR223W-A YBR224W YBR225W
YBR226C MCX1 SLX1 ROT2 YBR230C YBR230W-A
SWC5 YBR232C PBP2 DAD3 ARC40 YBR235W ABD1
YBR225W YBR226C MCX1 SLX1 ROT2 YBR230C
YBR230W-A SWC5 YBR232C PBP2 DAD3 ARC40
YBR235W ABD1 PRP5 YBR238C YBR239C THI2
YBR241C YBR242W ALG7 GPX2
GPX2 ISW1 YBR246W ENP1 HIS7 ARO4 YBR250W
MRPS5 DUT1 SRB6 TRS20 YBR255C-A YBR255W
DUT1 SRB6 TRS20 YBR255C-A YBR255W RIB5 POP4
SHG1 YBR259W RGD1 YBR261C FMP51 SHM1
YPT10 TSC10 SLM6 REI1 MRPL37
RIB5 POP4 SHG1 YBR259W RGD1 YBR261C FMP51
SHM1 YPT10 TSC10 SLM6 REI1 MRPL37 FMP21
YBR270C YBR271W HSM3 UBX7
FMP51 SHM1 YPT10 TSC10 SLM6 REI1 MRPL37
FMP21 YBR270C YBR271W HSM3 UBX7 CHK1 RIF1
PPS1 YBR277C DPB3 PAF1 YBR280C
RIF1 PPS1 YBR277C DPB3 PAF1 YBR280C YBR281C
MRPL27 SSH1 YBR284W YBR285W APE3 ZSP1 APM3
SNF5 BSD2
FYV5 YCL058W-A KRR1 MRC1 YCL062W VAC17
CHA1 YCL065W HMLALPHA1 HMLALPHA2
YCL068C YCL069W YCL073C YCLX01W
GID7 GLK1 YCL041C YCL042W PDI1 YCL044C
YCL045C YCL046W YCL047C SPS22 YCL049C APA1
LRE1 PBN1 YCLX03C YCLX04W
STE50 YCL033C LSB5 GRX1 GFD2 SRO9 ATG22
GID7 GLK1 YCL041C YCL042W PDI1 YCL044C
YCL045C YCL046W YCLX04W YCLX05C
YCL026C-B FUS1 RNQ1 BIK1 HIS4 RRP7 STE50
YCL033C LSB5 GRX1 GFD2 SRO9 ATG22 YCLX05C
YCLX06C YCLX07W
YCL020W YCL021W YCL021W-A YCL022C YCL023C
KCC4 AGP1 YCL026C FRM2 YCL026C-B FUS1 RNQ1
BIK1 HIS4 RRP7 YCLX06C YCLX07W YCLX08C
YCLX09W
YCL012C YCL012W YCL013W BUD3 DCC1 NFS1
LEU2 YCL019W YCL020W YCL021W YCL021W-A
YCL022C YCL023C KCC4 AGP1 YCL026C FRM2
YCL026C-B FUS1 RNQ1 BIK1 YCLX06C YCLX07W
YCLX08C YCLX09W YCLX10C
RER1 YCL001W-A YCL001W-B YCL002C PGS1
YCL005W VMA9 YCL006C YCL007C STP22 ILV6
SGF29 GBP2 YCL012C YCL012W YCL013W BUD3
DCC1 NFS1 LEU2 YCLX10C YCLX11W YCLX12W
RHB1 FEN2 RIM1 YCR029C SYP1 RPS14A BPH1
SNT1 FEN1 RRP43 RBK1 PHO87 BUD5 YCR038W-A
M3_209932_2107
48
3
209932
210748
M3_228125_2281
25
3
228125
228125
M3_240265_2403
31
3
240265
240331
M3_258267_2642
74
3
258267
264274
M3_301446_3014
46
3
301446
301446
M4_17718_17718
4
17718
17718
M4_33214_33214
4
33214
33214
M4_45364_54225
4
45364
54225
M4_62319_80849
4
62319
80849
M4_85846_10689
2
4
85846
106892
M4_114155_1222
93
4
114155
122293
M4_137412_1554
54
4
137412
155454
M4_161196_1650
32
4
161196
165032
M4_178037_1922
48
4
178037
192248
M4_201395_2263
17
4
201395
226317
M4_246738_2627
4
246738
262796
MATALPHA2 MATALPHA1 YCR041W TAF2
YCR043C PER1 YCR045C YCR045W-A IMG1 BUD23
YCRX03C YCRX05W YCRX07W
MATALPHA1 YCR041W TAF2 YCR043C PER1
YCR045C YCR045W-A IMG1 BUD23 YCR047W-A
ARE1 YCR049C YCR050C YCR051W RSC6 THR4
CTR86 YCRX05W YCRX07W
CTR86 YCR056W PWP2 YIH1 TAH1 YCR061W
YCR062W BUD31 YCR064C HCM1 RAD18 SED4
ATG15 YCRX10W
RAD18 SED4 ATG15 CPR4 IMG2 YCR072C SSK22
SOL2 ERS1 YCR075W-A YCR076C YCRX10W
YCRX12W YCRX13W YCRX14W
ERS1 YCR075W-A YCR076C PAT1 YCR079W
YCR081C-A SRB8 AHC2 TRX3 TUP1 YCR085W CSM1
YCR087C-A YCR087W ABP1 FIG2 YCR090C
YCRX14W YCRX15W YCRX16C YCRX18C
HMRA2 HMRA1 YCR097W-A YCR097WA
YCR097WB GIT1 YCR099C YCR100C YCR101C
YCR102C YCR102W-A YCR103C PAU3 ADH7
ADY3 YDL240C-A LRG1 YDL241W YDL242W AAD4
THI13 HXT15 SOR2
PTP1 BRE4 OST4 YDL233W GYP7 YPD1 PHO13
YDL237W GUD1 ADY3 LRG1
CDC13 YDL221W FMP45 HBT1 WHI4 SHS1 GCS1 HO
YDL228C SSB1 PTP1 BRE4 OST4 YDL233W
GLE1 NHP2 CWC2 UGA4 YDL211C SHR3 NOP6 PRR2
GDH2 RRI1 TIM22 YDL218W DTD1 CDC13 YDL221W
FMP45 HBT1 WHI4 SHS1
ARF1 YDL193W SNF3 SEC31 YDL196W ASF2 GGC1
YDL199C MGT1 TRM8 MRPL11 YDL203C RTN2
HEM3 YDL206W GLE1 NHP2 CWC2 UGA4 YDL211C
SHR3 NOP6
YDL183C RPL41A YDL185C-A TFP1 YDL186W
YDL187C PPH22 RBS1 UFD2 RPL35A ARF1
YDL193W SNF3 SEC31 YDL196W ASF2
CDC36 FAP7 NRP1 SFA1 UGX2 UGA3 GLT1
YDL172C YDL173W DLD1 AIR2 YDL176W YDL177C
DLD2 PCL9 YDL180W INH1 LYS20 YDL183C RPL41A
TFP1
YDL157C YDL158C YDL159C-B STE7 YDL159W-A
DHH1 YDL160C-A ENT1 YDL162C YDL163W CDC9
CDC36 FAP7 NRP1 SFA1 UGX2 UGA3 GLT1
CRD1 CCT4 YDL144C COP1 YDL146W RPN5 NOP14
ATG9 RPC53 BUD30 YDL152W SAS10 MSH5 CLB3
YDL156W YDL157C YDL158C YDL159C-B STE7
YDL159W-A DHH1 YDL160C-A ENT1
PCL2 VCX1 YDL129W RPP1B STF1 LYS21 CDC53
RPL41B YDL133W PPH21 RDI1 RPL35B ARF2 RGT2
SCM3 RPO21 BPL1 CRD1 CCT4 YDL144C COP1
YDL146W RPN5
PHO2 MSS2 KIN28 YDL109C YDL110C RRP42 TRM3
96
M4_263770_2738
46
4
263770
273846
M4_275191_2979
77
4
275191
297977
M4_304683_3096
25
4
304683
309625
M4_369365_3693
65
4
369365
369365
M4_432483_4780
80
4
432483
478080
4
509811
518400
4
527445
527517
4
555043
555043
M4_568122_5821
39
4
568122
582139
M4_582211_5822
11
4
582211
582211
M4_720990_7445
22
4
720990
744522
M4_782114_8028
51
4
782114
802851
M4_812947_8254
18
4
812947
825418
M4_843659_8436
59
4
843659
843659
4
864542
878291
4
926394
929895
4
935079
935079
M4_509811_5184
00
M4_527445_5275
17
M4_555043_5550
43
M4_864542_8782
91
M4_926394_9298
95
M4_935079_9350
ATG20 YDL114W YDL114W-A IWR1 NUP84 CYK3
YDL118W YDL119C YFH1 YDL121C UBP1 SNA4
YDL124W HNT1 CDC48
ARR4 DUN1 CDC2 QRI1 QRI7 QRI2 PHO2 MSS2
KIN28 YDL109C YDL110C RRP42 TRM3 ATG20
YDL114W YDL114W-A IWR1
RPS16B SUB2 YDL085C-A NDE2 YDL086C-A
YDL086W LUC7 ASM4 YDL089W RAM1 UBX3 SRP14
PMT5 YDL094C PMT1 YDL096C RPN6 SNU23
YDL099W ARR4 DUN1 CDC2 QRI1 QRI7 QRI2 PHO2
MSS2 KIN28 YDL109C
VAM6 MDH3 MRK1 THI3 RPP1A RPL13A RPS16B
SUB2 YDL085C-A NDE2 YDL086C-A YDL086W LUC7
ASM4 YDL089W RAM1
YDL041W SIR2 PRP11 MTF2 FAD1 MRP10 NPC2 SIT4
STP4 KNH1 YDL050C LHP1 SLC1 PBP4 MCH1
RMD1 NHP10 MCD1 ATP16 MED2 PTC1 RPT2 APC11
YDL009C YDL010W YDL011C YDL012C HEX3 NOP1
TSC13 YDL016C CDC7 ERP3 NTH1 YRB1 RCR2
YDR003W-A RAD57 MAF1 SOK1 TRP1 YDR008C
GAL3 YDR010C SNQ2 RPL4B PSF1 RAD61 YDR015C
DAD1 KCS1 YDR018C GCV1 YDR020C FAL1
YDR029W RAD28 YDR031W PST2 MRH1 LYS14
YDR034C-A YDR034W-B ARO3 EHD3 KRS1
YDR034C-A YDR034W-B ARO3 EHD3 KRS1 ENA5
ENA2 ENA1
HEM13 RPC11 BAP3 HEM12 YDR048C YDR049W
TPI1 YDR051C DBF4 YDR053W CDC34 PST1
DBF4 YDR053W CDC34 PST1 YDR056C YOS9 TGL2
UBC5 MAK21 YDR061W LCB2 YDR063W RPS13
YDR065W YDR066C YDR067C DOS2 DOA4 FMP16
PAA1 IPT1
YDR061W LCB2 YDR063W RPS13 YDR065W
YDR066C YDR067C DOS2 DOA4 FMP16 PAA1 IPT1
YDR128W SAC6 FIN1 YDR131C YDR132C YDR133C
YDR134C YCF1 VPS61 RGP1 HPR1 RUB1 MTQ2
DOP1 PEX7 SAN1 MKC7 TAF12 SWI5 EKI1 KGD2
SAC3 SSY1 YDR161W NBP2 CWC15 SEC1 TRM82
SEC5 TAF10 CDC37 STB3 YDR169C-A SEC7
YDR170W-A HSP42 SUP35 ARG82 HMO1
YDR170W-A HSP42 SUP35 ARG82 HMO1 RSM24
NGG1 UBC1 SDH4 CSN9 YDR179W-A SCC2 SAS4
CDC1 YDR182W-A YDR183C-A PLP1 ATC1 YDR185C
YDR186C
YDR186C YDR187C CCT6 SLY1 RVB1 HST4 NUP42
YDR193W MSS116 YDR194W-A REF2 YDR196C
CBS2 YDR198C
VPS64 SPC19 RAV2 YDR203W COQ4 MSC2 EBS1
UME6 MSS4 YDR209C YDR210W GCD6 TCP1
ADK1 SIR4 PCF11 IVY1 YDR230W COX20 HEM1
RTN1 LYS4 PRP42 FMN1 MRPL7 SEC26
IVY1 YDR230W COX20 HEM1 RTN1 LYS4 PRP42
79
M4_962693_9750
86
4
962693
975086
M4_1022764_103
9379
4
102276
4
103937
9
M4_1095532_110
9729
4
109553
2
110972
9
M4_1144476_114
9761
4
114447
6
114976
1
M4_1181160_118
8862
4
118116
0
118886
2
121341
6
124015
5
127273
7
129167
5
131038
0
132155
0
134455
0
121341
6
124024
5
127840
0
129167
5
131807
3
132155
0
134467
0
M4_1213416_121
3416
M4_1240155_124
0245
M4_1272737_127
8400
M4_1291675_129
1675
M4_1310380_131
8073
M4_1321550_132
1550
M4_1344550_134
4670
4
4
4
4
4
4
4
M4_1400033_140
9829
4
140003
3
140982
9
M4_1418647_141
8647
4
141864
7
141864
7
M4_1441486_145
6748
4
144148
6
145674
8
M4_1468373_147
4686
4
146837
3
147468
6
M4_1484268_149
1146
4
148426
8
149114
6
M4_1495582_149
7132
4
149558
2
149713
2
M4_1499294_150
7292
4
149929
4
150729
2
FMN1 MRPL7 SEC26 YDR239C SNU56
MNN10 TRS23 YDR246W-A VHS1 YDR248C
YDR249C YDR250C PAM1 BTT1 MET32 CHL4 RMD5
CTA1 SET7 HSP78 YAP6 SWM1 EXG2
PMP3 MTH1 YDR278C RNH202 RRP45 PHM6
YDR282C GCN2 DPP1 ZIP1 YDR286C YDR287W
NSE3 RTT103 YDR290W YDR291W SRP101 SSD1
TFB1 SSF2 PIB1 YDR314C IPK1 OMS1 YDR317W
MCM21 YDR319C SWA2 DAD4 YDR320W-B ASP1
TIM11 MRPL35 PEP7 UTP4 YCG1
SWR1 MSN5 YDR336W MRPS28 YDR338C YDR339C
YDR340W YDR341C HXT7
YPS7 TCM10 SBE2 YDR352W TRR1 YDR354C-A
TRP4 YDR355C SPC110 YDR357C GGA1 VID21
YDR360W BCP1 TFC6
CDC40 ESF1 YDR366C YDR367W YPR1 XRS2
YDR370C YDR371C-A CTS2 VPS74 FRQ1
YDR379C-A RGA2 ARO10 YDR381C-A YRA1 RPP2B
NKP1 ATO3 EFT2 MUS81 YDR387C
SXM1 YDR396W NCB2 UTP5 HPT1 URH1 YDR401W
DIT2 DIT1 RPB7 MRP20 PDR15 YDR406W-A TRS120
YDR406W-A TRS120 ADE8 SIZ1 STE14 DFM1
YDR412W YDR413C ERD1 YDR415C SYF1
YDR417C RPL12B RAD30 HKR1 ARO80 SIP1 CAD1
DYN2 SNX41 YDR426C RPN9 YDR428C TIF35 CYM1
ARO80 SIP1 CAD1 DYN2 SNX41 YDR426C RPN9
YDR428C TIF35 CYM1 YDR431W NPL3 YDR433W
PPZ2 YDR437W YDR438W LRS4 DOT1 APT2
YDR442W SSN2 YDR444W YDR445C ECM11
YDR464C-A SPP41 RMT2 PKH3 YDR467C TLG1 SDC1
UGO1 RPL27B TRS31 PRP3 YDR474C JIP4 YDR476C
SNF1 SNM1 PEX29 DIG2 PHO8
JIP4 YDR476C SNF1 SNM1 PEX29 DIG2 PHO8 CWC21
KRE2 VPS52 VPS72 VPS60
PKH1 YDR491C IZH1 FMP36 RSM28 VPS3 PUF6 ITR1
SEC20 LCD1 RPL37B PLM2 SAM2 LPP1 SPG3 PSP1
YDR506C GIN4
YDR506C GIN4 GNP1 YDR509W YDR510C-A SMT3
ACN9 EMI1 TTR1 YDR514C SLF1 EMI2 GRH1 EUG1
FPR2 YDR520C YDR521W SPS2
EMI2 GRH1 EUG1 FPR2 YDR520C YDR521W SPS2
SPS1 AGE1 YDR524C-A YDR524C-B YDR524W-A
API2 SNA2 YDR526C RBA50 HLR1 QCR7 APA2
YDR531W YDR532C
SPS1 AGE1 YDR524C-A YDR524C-B YDR524W-A
API2 SNA2 YDR526C RBA50 HLR1 QCR7 APA2
YDR531W YDR532C HSP31 FIT1 YDR535C
YDR524C-A YDR524C-B YDR524W-A API2 SNA2
YDR526C RBA50 HLR1 QCR7 APA2 YDR531W
YDR532C HSP31 FIT1 YDR535C STL1 YDR537C
PAD1 YDR539W
M4_1510883_152
5327
4
151088
3
152532
7
M5_5393_5400
5
5393
5400
M5_6335_17399
5
6335
17399
M5_25912_25918
5
25912
25918
M5_29073_30057
5
29073
30057
M5_40306_42420
5
40306
42420
M5_44605_48845
5
44605
48845
M5_73010_79653
5
73010
79653
M5_99004_99004
5
99004
99004
M5_109310_1177
05
5
109310
117705
M5_166032_1660
38
5
166032
166038
M5_183958_1963
52
5
183958
196352
M5_200734_2182
50
5
200734
218250
M5_222998_2230
04
5
222998
223004
M5_225483_2346
29
5
225483
234629
5
240105
244117
5
251262
251647
5
272255
272258
5
312672
321714
M5_240105_2441
17
M5_251262_2516
47
M5_272255_2722
58
M5_312672_3217
14
HSP31 FIT1 YDR535C STL1 YDR537C PAD1
YDR539W YDR540C YDR541C YDR542W YDR543C
YDR544C YDR545C-A YRF1-1
RMD6 YEL073C YEL074W YEL075C YEL075W-A
YEL076C YEL076C-A YEL076W-C YEL077C
YEL077W-A
HPA3 YEL067C YEL068C HXT13 DSF1 DLD3 RMD6
YEL073C YEL074W YEL075C YEL075W-A YEL076C
YEL076C-A YEL076W-C YEL077C YEL077W-A
NPR2 CAN1 AVT2 SIT1 HPA3 YEL067C YEL068C
HXT13 DSF1 DLD3
CIN8 NPR2 CAN1 AVT2 SIT1 HPA3 YEL067C
YEL068C HXT13 DSF1
POL5 HAT2 YEL057C PCM1 SOM1 YEL059W PRB1
CIN8 NPR2 CAN1 AVT2
VMA8 AFG1 MAK10 YEL053W-A RPL12A POL5
HAT2 YEL057C PCM1 SOM1 YEL059W PRB1 CIN8
NPR2
YEL032C-A MCM3 YEL033W YEL034C-A HYP2
UTR5 ANP1 RAD23 UTR4 CYC7 UTR2 YEL041W
GDA1 YEL043W IES6 YEL045C GLY1 YEL047C
YEL048C PAU2
RIP1 YEL025C SNU13 CUP5 YEL028W BUD16
YEL030C-A ECM10 SPF1
EDC3 YEL016C PMP2 GTT3 YEL018C-A EAF5
MMS21 YEL020C YEL020C-B TIM9 URA3 GEA2
YEL023C RIP1 YEL025C SNU13 CUP5
NOP16 PMI40 FMP52 YND1 YER006C-A NUG1 RBF20
PAC2 SEC3 NTF2 YER010C TIR1
TIR1 PRE1 PRP22 BUD25 HEM14 FAA2 BIM1 AFG3
SPC25 SBH2 ISC1 GPA2 RPN3 SRB4 YER023C-A
PRO3 YAT2 GCD11
SPC25 SBH2 ISC1 GPA2 RPN3 SRB4 YER023C-A
PRO3 YAT2 GCD11 CHO1 GAL83 MIG3 SMB1
YER030W YPT31 FIR1 ZRG8 YER034W EDC2 ARB1
PHM8 KRE29
YER030W YPT31 FIR1 ZRG8 YER034W EDC2 ARB1
PHM8 KRE29 FMP49 HVG1 YER039C-A GLN3
FIR1 ZRG8 YER034W EDC2 ARB1 PHM8 KRE29
FMP49 HVG1 YER039C-A GLN3 YEN1 MXR1 SAH1
ERG28 MEI4 ACA1 SPO73 YER046W-A
GLN3 YEN1 MXR1 SAH1 ERG28 MEI4 ACA1 SPO73
YER046W-A SAP1 CAJ1 YER048W-A YER049W
SPO73 YER046W-A SAP1 CAJ1 YER048W-A
YER049W RSM18 YER051W HOM3 PIC2 YER053C-A
GIP2 HIS1 FCY2 RPL34A HMF1 PET117 PCL6 FCY21
FCY22 CEM1 HOR2 THO1
VTC1 ALD5 RPS24A YER074W-A PTP3 YER076C
YER076W-A YER077C YER078C YER078W-A
YER079C-A YER079W FMP29 SER3 UTP7 RMD7
YER084W YER084W-A YER085C ILV1 YER087W
M5_332264_3332
52
5
332264
333252
5
350744
350744
5
395442
395442
5
420595
430931
M5_458085_4580
85
5
458085
458085
M5_468641_4686
41
5
468641
468641
M5_480051_4835
38
5
480051
483538
M5_492125_5047
17
5
492125
504717
5
511793
525380
5
530758
538875
5
546664
549142
M5_553222_5687
34
5
553222
568734
M6_5152_5153
6
5152
5153
M6_5852_5880
6
5852
5880
M6_5961_5961
6
5961
5961
M6_15106_33688
6
15106
33688
M6_38648_48224
6
38648
48224
M6_57455_57455
6
57455
57455
M6_70818_75460
6
70818
75460
M6_78241_84403
6
78241
84403
M6_100263_1073
6
100263
107364
M5_350744_3507
44
M5_395442_3954
42
M5_420595_4309
31
M5_511793_5253
80
M5_530758_5388
75
M5_546664_5491
42
SER3 UTP7 RMD7 YER084W YER084W-A YER085C
ILV1 YER087C-A SBH1 YER087W DOT6 YER088C-A
YER088W-B PTC2 TRP2 MET6 YER091C-A IES5
MET6 YER091C-A IES5 TSC11 YER093C-A PUP3
RAD51 SHC1 YER097W UBP9 PRS2 UBC6
LSM4 YER113C BOI2 SPR6 SLX8 RPL23B SHO1
AVT6 YER119C-A SCS2 YER121W GLO3
RSP5 NSA2 LCP5 YER128W PAK1 YER130C RPS26B
PMD1 GLC7 YER133W-A YER134C YER135C GDI1
YER138W-A YER139C YER140W COX15 MAG1 DDI1
UBP5 FTR1 YER145C-A LSM5 SCC4 YER147C-A
SPT15 YER148W-A PEA2
UBP5 FTR1 YER145C-A LSM5 SCC4 YER147C-A
SPT15 YER148W-A PEA2 SPI1 UBP3 YER152C
YER152W-A PET122 OXA1
UBP3 YER152C YER152W-A PET122 OXA1 BEM2
YER156C COG3 YER158C YER158W-A BUR6
YER156C COG3 YER158C YER158W-A BUR6
YER160C SPT2 RAD4 YER163C CHD1 YER165C-A
PAB1
YER163C CHD1 YER165C-A PAB1 DNF1 BCK2 CCA1
RPH1 ADK2 RAD3 BRR2
CCA1 RPH1 ADK2 RAD3 BRR2 YER172C-A RAD24
GRX4 TMT1 YER175W-A ECM32 BMH1 PDA1
RAD24 GRX4 TMT1 YER175W-A ECM32 BMH1 PDA1
DMC1 ISC10 SLO1 YER181C FMP10 FAU1 YER184C
ECM32 BMH1 PDA1 DMC1 ISC10 SLO1 YER181C
FMP10 FAU1 YER184C YER185W YER186C
YER186W-A YER187W YER188C-A YER188W
YER189W YER190C-A YER190C-B YRF1-2
AAD6 AAD16 THI5 SNZ3 SNO3 DDI2 COS4 YFL063W
YFL064C YFL065C YFL066C YFL067W YFL068W
FMP32 RGD2 EMP47 YFL049W ALR2 YFL051C
YFL052W DAK2 YFL054C AGP3 AAD6 AAD16 THI5
SNZ3 SNO3 DDI2 COS4 YFL063W
TUB2 YPT1 ACT1 YFL040W FET5 YFL041W-A
YFL042C YFL043C YOD1 SEC53 FMP32 RGD2 EMP47
YFL049W ALR2 YFL051C YFL052W
RPL22B MOB2 YFL034W YFL035C YFL035C-A
YFL035C-B RPO41 TUB2 YPT1 ACT1 YFL040W FET5
YFL041W-A
STE2 GYP8 CAF16 CAK1 AGX1 YFL031C-A HAC1
YFL032W RIM15 RPL22B MOB2 YFL034W YFL035C
YFL035C-A YFL035C-B
FRS2 BUD27 EPL1 BST1 STE2 GYP8 CAF16 CAK1
AGX1 YFL031C-A HAC1 YFL032W RIM15
CDC4 WWM1 AUA1 HXT10 YFL011W-A YFL012W
64
M6_134096_1610
65
6
134096
161065
M6_167184_1725
72
6
167184
172572
M6_172578_1773
23
6
172578
177323
M6_205881_2086
54
6
205881
208654
M6_226146_2276
75
6
226146
227675
M6_232259_2343
49
6
232259
234349
M6_238758_2428
76
6
238758
242876
M6_244292_2536
90
6
244292
253690
M6_253696_2639
89
6
253696
263989
M7_3714_23129
7
3714
23129
M7_44996_44996
7
44996
44996
M7_52613_52613
7
52613
52613
M7_55458_55464
7
55458
55464
M7_69250_73488
7
69250
73488
M7_85112_85112
7
85112
85112
M7_92848_93397
7
92848
93397
M7_98231_11790
0
7
98231
117900
M7_128898_1398
7
128898
139851
YFL012W-A IES1 YFL013W-A HSP12 YFL015C
YFL015W-A MDJ1 GNA1 SMX2 LPD1 YFL018W-A
YFL019C PAU5 YFL021C-A GAT1 FRS2 BUD27
DEG1 SPB4 YFL002W-A MSH4 VTC2 SEC4 YFL006W
BLM3 LOC1 NIC96 YPI1 RPN11 SAD1 YFR006W
YFR007W FAR7 GCN20 YFR009W-A UBP6 YFR010WA YFR011C YFR012W YFR012W-A
YFR007W FAR7 GCN20 YFR009W-A UBP6 YFR010WA YFR011C YFR012W YFR012W-A IOC3 CMK1 GSY1
YFR016C YFR017C
GCN20 YFR009W-A UBP6 YFR010W-A YFR011C
YFR012W YFR012W-A IOC3 CMK1 GSY1 YFR016C
YFR017C YFR018C
YFR022W PES4 YFR024C LSB3 HIS2 YFR026C ECO1
CDC14 PTR3 MET10 SMC2
SMC2 RPL2A YFR032C RPL29 YFR032C-B QCR6
PHO4 YFR034W-A YFR035C CDC26 YFR036W-A
RSC8 YFR038W YFR039C SAP155
YFR032C RPL29 YFR032C-B QCR6 PHO4 YFR034W-A
YFR035C CDC26 YFR036W-A RSC8 YFR038W
YFR039C SAP155 ERJ5 YFR042W YFR043C YFR044C
YFR045W CNN1
YFR038W YFR039C SAP155 ERJ5 YFR042W YFR043C
YFR044C YFR045W CNN1 BNA6 RMD8 YMR31 PRE4
RET2
SAP155 ERJ5 YFR042W YFR043C YFR044C YFR045W
CNN1 BNA6 RMD8 YMR31 PRE4 RET2 YFR052C-A
RPN12 HXK1 YFR054C
BNA6 RMD8 YMR31 PRE4 RET2 YFR052C-A RPN12
HXK1 YFR054C YFR055W YFR056C YFR057W
YGL250W HFM1 RTG2 HXK2 FZF1 ZRT1 ADH4
MNT2 YGL258W YGL258W-A YPS5 YGL260W
YGL261C YGL262W COS12
MTO1 HAP2 CSE1 YGL239C DOC1 KAP114 YGL242C
TAD1 RTF1 GUS1 RAI1 BRR6 PDE1
TAN1 SEC15 ADE5,7 YGL235W MTO1 HAP2 CSE1
YGL239C DOC1 KAP114 YGL242C TAD1
YGL230C YGL231C TAN1 SEC15 ADE5,7 YGL235W
MTO1 HAP2 CSE1 YGL239C DOC1 KAP114
YGL220W NIF3 EDC1 COG1 SDT1 VRG4 OST5
YGL226W VID30 SHE10 SAP4 YGL230C YGL231C
TAN1 SEC15
YPT32 YGL210W-A NCS6 VAM7 SKI8 YGL214W
CLG1 KIP3 YGL217C SRF1 MDM34 YGL220W NIF3
EDC1 COG1 SDT1 VRG4
SPT16 SIP2 MIG2 YPT32 YGL210W-A NCS6 VAM7
SKI8 YGL214W CLG1 KIP3 YGL217C SRF1 MDM34
MDS3 YIP4 YGL199C EMP24 MCM6 ARO8 KEX1
YGL204C POX1 CHC1 SPT16 SIP2 MIG2 YPT32
YGL210W-A NCS6 VAM7 SKI8 YGL214W CLG1
YGL188C YGL188C-A RPS26A CDC55 COX13 IME4
51
YGL193C HOS2 GCN1 YGL196W MDS3 YIP4
YGL199C EMP24 MCM6
YGL185C TPN1 COX4 YGL188C YGL188C-A RPS26A
CDC55 COX13 IME4 YGL193C HOS2 GCN1
YGL160W YIP5 SUT1 RAD54 YRB30 YGL165C CUP2
PMR1 HUR1 SUA5 SPO74 ROK1 NUP49 KEM1 BUD13
SAE2 YGL176C YGL177W MPT5 TOS3 ATG1 GTS1
AMS1 YGL157W RCK1 YGL159W YGL160W YIP5
SUT1 RAD54 YRB30
CEG1 SNT2 YGL132W ITC1 PCL10 RPL1B MRM2
SEC27 YGL138C
YGL102C RPL28 VPS73 ARC1 MLC1 RMD9 YGL108C
YGL109W CUE3 NSA1 TAF6 SLD3 YGL114W SNF4
SRM1 USE1 LSG1 SEH1 YGL101W YGL102C RPL28
VPS73 ARC1 MLC1 RMD9 YGL108C YGL109W CUE3
YGL063C-A PUS2 MRH4 ALG2 SGF73 NPY1 MNP1
SRF3 RPB9 RCS1 YGL072C HSF1 YGL074C MPS2
YGL039W HEM2 YGL041C YGL041C-B YGL041W-A
YGL042C DST1 RNA15 RIM8 YGL046W YGL047W
RPT6 TIF4632 YGL050W MST27 YGL052W PRM8
ERV14 OLE1 SDS23 YGL057C RAD6 YGL059W
AGA2 HOP2 YGL034C MIG1 YGL036W PNC1 OCH1
YGL039W HEM2 YGL041C YGL041C-B YGL041W-A
YGL042C DST1 RNA15
CWH41 SCW11 CGR1 RPL30 RPL24A AGA2 HOP2
YGL034C MIG1 YGL036W PNC1 OCH1 YGL039W
PDR1 YGL014C-A PUF4 YGL015C KAP122 ATE1
JAC1 CKB1 MDM39 ALK1 STT3 PIB2 SST3 PGD1
TRP5 CWH41 SCW11 CGR1
ERG26 ERP6 CDH1 RPN14 COG7 PMC1 YGL006W-A
YGL007C-A YGL007W PMA1 YGR001C SWC4 CUL3
PEX31 TFG2 PRP18 MUQ1 STF2 SEC9 NMA2
YGR011W YGR012W SNU71 MSB2 YGR015C
YGR016W YGR017W
SNU71 MSB2 YGR015C YGR016W YGR017W
YGR018C UGA1 VMA7 YGR021W YGR022C MTL1
THG1 YGR025W YGR026W RPS25A
YGR015C YGR016W YGR017W YGR018C UGA1
VMA7 YGR021W YGR022C MTL1 THG1 YGR025W
YGR026W RPS25A MSP1 ERV1 POP6 YGR031C-A
YGR031W GSC2 FMP17 RPL26B YGR035C
YGR035W-A CAX4 ACB1 ORM1
RME1 YGR045C YGR046W TFC4 UFD1 SCM4
YGR050C YGR051C FMP48 YGR053C YGR054W
MUP1
COX18 SPT4 YGR064W VHT1 YGR066C YGR067C
YGR068C YGR068W-A YGR069W ROM1 YGR071C
UPF3
M7_141949_1437
62
7
141949
143762
M7_167587_1921
40
7
167587
192140
7
202131
202131
7
256953
256953
7
301131
301813
7
311205
312740
7
375499
375499
M7_402833_4155
85
7
402833
415585
M7_425445_4274
76
7
425445
427476
M7_431858_4358
64
7
431858
435864
M7_449898_4609
45
7
449898
460945
M7_490784_5143
08
7
490784
514308
M7_524216_5293
76
7
524216
529376
M7_530473_5572
36
7
530473
557236
M7_592983_5929
83
7
592983
592983
M7_625404_6254
04
7
625404
625404
7
656248
656248
MRP13 RPL11B PIL1 PDC6 CTT1 NNF2 UTP22
7
682389
697549
VAS1 RRP46 TPC1 ASK10 ESP1 TEL2 MDR1 PCP1
M7_202131_2021
31
M7_256953_2569
53
M7_301131_3018
13
M7_311205_3127
40
M7_375499_3754
99
M7_656248_6562
48
M7_682389_6975
49
M7_705697_7056
97
M7_707605_7082
61
M7_708285_7082
85
M7_708345_7120
04
7
705697
705697
7
707605
708261
7
708285
708285
7
708345
712004
M7_787743_7951
52
7
787743
795152
M7_804945_8234
28
7
804945
823428
M7_833786_8337
86
7
833786
833786
M7_853749_8655
75
7
853749
865575
M7_880301_9001
34
7
880301
900134
M7_905017_9130
77
7
905017
913077
M7_916471_9196
54
7
916471
919654
M7_940458_9485
90
7
940458
948590
7
951969
956838
7
974625
974680
M7_985414_9958
92
7
985414
995892
M7_1007539_100
7589
7
100753
9
100758
9
M7_1048152_105
7540
7
104815
2
105754
0
M7_1058947_106
3841
7
105894
7
106384
1
M7_1071420_108
3245
7
107142
0
108324
5
M8_5776_19171
8
5776
19171
M7_951969_9568
38
M7_974625_9746
80
YGR102C NOP7 SRB5 VMA21 YGR106C YGR107W
CLB1 CLB6
NOP7 SRB5 VMA21 YGR106C YGR107W CLB1 CLB6
YGR110W
SRB5 VMA21 YGR106C YGR107W CLB1 CLB6
YGR110W YGR111W SHY1
VMA21 YGR106C YGR107W CLB1 CLB6 YGR110W
YGR111W SHY1
VMA21 YGR106C YGR107W CLB1 CLB6 YGR110W
YGR111W SHY1 DAM1 YGR114C YGR115C
THI4 ENP2 YGR146C YGR146C-A NAT2 RPL24B
YGR149W YGR150C YGR151C RSR1 YGR153W
YGR154C CYS4 PTI1 CHO2
RSR1 YGR153W YGR154C CYS4 PTI1 CHO2 MTR3
NSR1 YGR160W RTS3 TIF4631 GTR2 YGR164W
MRPS35 KRE11 CLC1
TIF4631 GTR2 YGR164W MRPS35 KRE11 CLC1
YGR168C PUS6 YGR169C-A PSD2 MSM1 YIP1
RBG2 CBP4 YGR174W-A ERG1 YGR176W ATF2 PBP1
OKP1 RNR4 TIM13 YGR182C QCR9 UBR1 TYS1 TFG1
HGH1 BUB1
HGH1 BUB1 CRH1 YGR190C HIP1 TDH3 PDX1 XKS1
SKI6 FYV8 SNG1 YGR198W PMT6 ELP2 YGR201C
PCT1 YGR203W YGR204C-A ADE3 YGR205W
YGR198W PMT6 ELP2 YGR201C PCT1 YGR203W
YGR204C-A ADE3 YGR205W YGR206W YGR207C
SER2 TRX2 YGR210C ZPR1 SLI1 RTA1 RPS0A RSM27
YGR204C-A ADE3 YGR205W YGR206W YGR207C
SER2 TRX2 YGR210C ZPR1 SLI1 RTA1 RPS0A RSM27
GPI1 CCH1
CRM1 YGR219W MRPL9 TOS2 PET54 HSV2 AZR1
AMA1 YGR226C DIE2 YGR228W SMI1 BNS1 PHB2
NAS6 PHO81
AZR1 AMA1 YGR226C DIE2 YGR228W SMI1 BNS1
PHB2 NAS6 PHO81 YHB1 YGR235C SPG1 YGR237C
KEL2 PEX21 PFK1 YGR240C-A YAP1802 YGR242W
FMP43 LSC2 SDA1 BRF1
YAP1802 YGR242W FMP43 LSC2 SDA1 BRF1 CPD1
SOL4 MGA1 YGR250C YGR251W GCN5 PUP2 ENO1
COQ6 GND2
PUP2 ENO1 COQ6 GND2 MTM1 RAD2 YGR259C
TNA1 APL6 BUD32
YGR272C YGR273C TAF1 RTT102 RNH70 YGR277C
CWC22 SCW4 PXR1 YOR1 BGL2 YGR283C ERV29
ZUO1 BIO2
SCW4 PXR1 YOR1 BGL2 YGR283C ERV29 ZUO1
BIO2 YGR287C MAL13
ZUO1 BIO2 YGR287C MAL13 MAL11 YGR290W
YGR291C MAL12 YGR293C YGR294W COS6
YGR296C-A YGR296C-B YRF1-3
MUP3 YHL037C CBP2 YHL039W ARN1 YHL041W
M8_45098_46007
8
45098
46007
M8_56246_63386
8
56246
63386
M8_71742_72233
8
71742
72233
M8_80014_95469
8
80014
95469
M8_98513_98513
8
98513
98513
M8_111679_1116
90
8
111679
111690
M8_128732_1400
58
8
128732
140058
M8_149336_1576
05
8
149336
157605
M8_161987_1769
94
8
161987
176994
M8_185012_1888
51
8
185012
188851
M8_193175_2092
45
8
193175
209245
M8_213595_2219
33
8
213595
221933
M8_224267_2242
67
8
224267
224267
8
293131
293131
8
312183
324050
8
340251
340251
8
389044
399409
M8_293131_2931
31
M8_312183_3240
50
M8_340251_3402
51
M8_389044_3994
YHL042W ECM34 YHL044W YHL045W YHL046C
YHL046W-A ARN2 YHL048C-A COS8 YHL049C
YHL050C YHL050W-A
SNF6 YHL026C RIM101 WSC4 YHL029C ECM29
YHL030W-A GOS1 GUT1 RPL8A
DUR3 YHL017W YHL018W APM2 YHL019W-A OPI1
FMP12 SPO11 RMD11 RIM4 SNF6 YHL026C RIM101
WSC4 YHL029C
PRS3 YHL012W YHL013C YLF2 RPS20 YHL015W-A
DUR3 YHL017W YHL018W APM2 YHL019W-A OPI1
FMP12 SPO11
RPL14B YHL002C-A HSE1 LAG1 MRP4 YHL005C
SHU1 YHL006W-A STE20 YHL008C YAP3 YHL010C
PRS3 YHL012W YHL013C YLF2 RPS20 YHL015W-A
DUR3 YHL017W
RPL14B YHL002C-A HSE1 LAG1 MRP4 YHL005C
SHU1 YHL006W-A STE20 YHL008C OSH7 QCR10
RPL14B YHL002C-A HSE1 OSH7 QCR10 LEU5
YHR003C NEM1 GPA1 MRS11 STP2 ERG11
ERG11 YHR007C-A SOD2 YHR009C RPL27A DIA4
VPS29 ARD1 SPO13 MIP6 YSC84 YSC83 ARG4
DED81 YHR020W RPS27B ECM12 YHR022C
ARG4 DED81 YHR020W RPS27B ECM12 YHR022C
YHR022C-A MYO1 MAS2 THR1 PPA1 RPN1 DAP2
YHR028W-A
MYO1 MAS2 THR1 PPA1 RPN1 DAP2 YHR028W-A
YHR029C SLT2 RRM3 YHR032C-A YHR032W
YHR032W-A YHR033W PIH1 YHR035W YHR036W
PUT2 RRF1 MSC7
YHR032C-A YHR032W-A YHR033W PIH1 YHR035W
YHR036W PUT2 RRF1 MSC7 VMA10 YHR039C-B
BCD1 SRB2 NCP1 DOG2 DOG1 YHR045W INM1
RRF1 MSC7 VMA10 YHR039C-B BCD1 SRB2 NCP1
DOG2 DOG1 YHR045W INM1 AAP1' YHR048W
YHR049C-A FSH1 SMF2 YHR050W-A COX6 CIC1
YHR052W-A CUP1-1 YHR054C YHR054W-A CUP1-2
RSC30 YHR056W-A CPR2
YHR048W YHR049C-A FSH1 SMF2 YHR050W-A
COX6 CIC1 YHR052W-A CUP1-1 YHR054C
YHR054W-A CUP1-2 RSC30 YHR056W-A CPR2 MED6
FYV4 VMA22 GIC1 RPP1 PAN5 YHR063W-A SSZ1
RRP3 SSF1 HTD2
YHR054W-A CUP1-2 RSC30 YHR056W-A CPR2 MED6
FYV4 VMA22 GIC1 RPP1 PAN5 YHR063W-A SSZ1
RRP3 SSF1 HTD2 DYS1 RRP4
YNG2 MSR1 HXT4 AHT1 HXT1 YHR095W HXT5
YHR097C SFB3
TRA1 YHR100C BIG1 KIC1 SBE22 GRE3 YPT35 TRR2
CDC12 GGA2 CTM1 ERP5 UBA4
CTM1 ERP5 UBA4 YHR112C YHR113W BZZ1 DMA1
COX23 TOM71 ORC6 SET1
YHR139C-A YHR140W RPL42B CHS7 DSE2 RPC10
09
DCD1 YHR145C CRP1 MRPL6 IMP3 SKG6 PEX28
YHR151C SPO12 SPO16 RTT107 YHR155W
SPO12 SPO16 RTT107 YHR155W LIN1 REC104 KEL1
YHR159W PEX18
YAP1801 YHR162W SOL3 DNA2 PRP8 YHR165W-A
CDC23 THP2 MTG2 DBP8 NMD3 ATG7 SPC97
YHR173C
SPC97 YHR173C ENO2 CTR2 YHR175W-A FMO1
YHR177W STB5 OYE2 YHR180C-B YHR180W
YHR180W-A SVP26
M8_410845_4109
89
8
410845
410989
M8_430123_4417
90
8
430123
441790
M8_457580_4575
80
8
457580
457580
8
518539
521046
SCH9 SKN7 SET5 BAT1 YHR209W YHR210C FLO5
8
525546
525546
SET5 BAT1 YHR209W YHR210C FLO5
8
525555
525555
8
525664
525664
8
525668
525668
8
525673
525673
M8_549634_5496
38
8
549634
549638
M9_19607_19650
9
19607
19650
M9_21454_21455
9
21454
21455
M9_27026_38608
9
27026
38608
M9_45863_47053
9
45863
47053
M9_61273_88155
9
61273
88155
M9_98949_13684
5
9
98949
136845
9
139462
141014
9
154733
155027
9
190794
205191
M8_518539_5210
46
M8_525546_5255
46
M8_525555_5255
55
M8_525664_5256
64
M8_525668_5256
68
M8_525673_5256
73
M9_139462_1410
14
M9_154733_1550
27
M9_190794_2051
91
YHR213W-A YHR213W-B YHR214C-D YHR214C-E
YHR214W YHR214W-A YHR214C-B PHO12 IMD2
YHR217C YHR218W
YIL168W YIL169C YIL170W YIL171W YIL171W-A
YIL172C VTH1
YIL167W YIL168W YIL169C YIL170W YIL171W
YIL171W-A YIL172C VTH1
YIL156W-A YIL156W-B FMP35 YIL158W BNR1 POT1
YIL161W SUC2 YIL163C NIT1 YIL165C YIL166C
YIL167W YIL168W YIL169C YIL170W YIL171W
YIL171W-A YIL172C
YIL152W RRD1 IMP2' GUT2 UBP7 YIL156W-A
YIL156W-B FMP35 YIL158W BNR1 POT1 YIL161W
SUC2 YIL163C
YIL134C-A FLX1 VHS2 OM45 RBF108 TPM2 REV7
AXL2 YIL141W YIL142C-A CCT2 SSL2 TID3 PAN6
ECM37 SLN1 RPL40A MLP2 MCM10 YIL151C
YIL152W RRD1 IMP2' GUT2
NUP159 YIL115W-A HIS5 PRM5 RHO3 RPI1 QDR1
QDR2 POG1 SIM1 AYR1 KGD1 STH1 YIL127C MET18
TAO3 YIL130W FKH1 CSM2 RPL16A YIL134C-A
FLX1 VHS2 OM45 RBF108 TPM2
SDP1 POR2 NUP159 YIL115W-A HIS5 PRM5 RHO3
RPI1 QDR1 QDR2 POG1
PFK26 YIL108W SEC24 YIL110W COX5B HOS4 SDP1
POR2 NUP159
THS1 AIR1 YIL080W YIL082W YIL082W-A YIL083C
SDS3 KTR7 YIL086C YIL087C AVT7 YIL089W
YIL090W YIL091C YIL092W RSM25 LYS12 PRK1
M9_214482_2547
45
9
214482
254745
M9_257943_2595
33
9
257943
259533
M9_268352_2684
12
9
268352
268412
M9_272372_2834
68
9
272372
283468
M9_289503_2964
53
9
289503
296453
M9_308848_3254
28
9
308848
325428
M9_334195_3412
16
9
334195
341216
M9_362631_3720
93
9
362631
372093
M9_386046_3980
74
9
386046
398074
M9_399057_4100
28
9
399057
410028
M9_415311_4200
76
9
415311
420076
M9_425547_4370
63
9
425547
437063
M10_22213_3409
8
10
22213
34098
10
36810
36810
10
39595
40238
10
43261
51003
M10_36810_3681
0
M10_39595_4023
8
M10_43261_5100
YIL096C FYV10
NEO1 DFG10 PCL7 MMF1 RPL34B RHR2 YIL054W
YIL055C YIL056W YIL057C YIL058W YIL059C
YIL060W SNP1 ARC15 YRB2 YIL064W FIS1 RNR3
YIL066W-A YIL067C SEC6 YIL068W-A RPS24B
MAM33 PCI8 YIL071W-A HOP1 SPO22 SER33 RPN2
SEC28 YIL077C THS1 AIR1 YIL080W YIL082W
YIL082W-A
YIL046W-A SYG1 YIL047C-A NEO1 DFG10 PCL7
MMF1 RPL34B RHR2 YIL054W YIL055C YIL056W
YIL057C
APQ12 GVP36 YIL042C CBR1 AGE2 PIG2 MET30
YIL046W-A SYG1 YIL047C-A NEO1 DFG10 PCL7
YIL032C BCY1 CAP2 CKA1 CST6 PRM2 NOT3
YIL039W APQ12 GVP36 YIL042C CBR1 AGE2 PIG2
MET30 YIL046W-A SYG1 YIL047C-A NEO1
IRR1 KRE27 YIL028W YIL029C YIL029W-A SSM4
YIL030W-A ULP2 YIL032C BCY1 CAP2 CKA1 CST6
PRM2 NOT3
DOT5 TIR3 YIL012W PDR11 YIL014C-A MNT3 BAR1
YIL015C-A SNL1 VID28 RPL2B FAF1 HIS6 YIL020CA YIL021C-A RPB3 TIM44 YIL023C YIL024C YIL025C
IRR1 KRE27 YIL028W YIL029C YIL029W-A
YIL002W-A CFD1 BET1 EPS1 YIL006W NAS2 URM1
EST3 FAA3 DOT5 TIR3 YIL012W PDR11 YIL014C-A
MNT3 YIL015C-A
YIL001W SGN1 MPH1 YIR003W DJP1 IST3 PAN1
YIR007W PRI1 MSL1 DSN1 STS1 SQT1 GAT4
YIR014W
DSN1 STS1 SQT1 GAT4 YIR014W RPR2 YIR016W
MET28 YIR017W-A YIR018C-A YAP5 MUC1 YIR020C
YIR020C-B YIR020W-A YIR020W-B MRS1 YIR021WA SEC11 YIR023C-A DAL81 YIR024C MND2 YVH1
DAL1
MUC1 YIR020C YIR020C-B YIR020W-A YIR020W-B
MRS1 YIR021W-A SEC11 YIR023C-A DAL81 YIR024C
MND2 YVH1 DAL1 DAL4 DAL2 DCG1 YIR030W-A
DAL7 DAL3 MGA2
YVH1 DAL1 DAL4 DAL2 DCG1 YIR030W-A DAL7
DAL3 MGA2 LYS1 YIR035C YIR036C YIR036W-A
HYR1 GTT1
MGA2 LYS1 YIR035C YIR036C YIR036W-A HYR1
GTT1 YPS6 YIR040C YIR041W YIR042C YIR043C
YIR044C
NUC1 CBP1 PEX2 YJL211C OPT1 YJL213W HXT8
YJL215C YJL216C YJL217W YJL218W HXT9
YJL220W FSP2 VTH2
YJL207C NUC1 CBP1 PEX2 YJL211C OPT1 YJL213W
HXT8
YJL206C YJL207C NUC1 CBP1 PEX2 YJL211C OPT1
YJL213W
MBB1 YJL200C ECM25 YJL202C PRP21 RCY1
3
M10_56788_6957
8
10
56788
69578
M10_76840_8565
4
10
76840
85654
M10_87113_8711
3
10
87113
87113
M10_89097_9637
6
10
89097
96376
M10_99891_1011
93
10
99891
101193
M10_110038_138
712
10
110038
138712
M10_147750_159
479
10
147750
159479
M10_163850_185
319
10
163850
185319
M10_191571_191
768
10
191571
191768
10
204137
204137
10
214773
227894
10
259991
262593
M10_307178_307
178
10
307178
307178
M10_325500_330
465
10
325500
330465
M10_336317_353
027
10
336317
353027
M10_372838_372
10
372838
372838
M10_204137_204
137
M10_214773_227
894
M10_259991_262
593
NCE101 YJL206C YJL206C-A YJL207C NUC1 CBP1
PEX2 YJL211C OPT1
SWE1 BUD19 RPL39 RPS22A RPS14B SOP4 YJL193W
CDC6 YJL195C ELO1 YJL197C-A UBP12 PHO90
MBB1 YJL200C ECM25 YJL202C PRP21 RCY1
NCE101 YJL206C YJL206C-A
KRE9 YJL175W SWI3 RPL17B ATG27 PFD1 ATP12
YJL181W YJL182C MNN11 GON7 YJL185C MNN5
SWE1 BUD19 RPL39 RPS22A RPS14B SOP4 YJL193W
CDC6 YJL195C ELO1
RFA3 KRE9 YJL175W SWI3 RPL17B ATG27 PFD1
ATP12 YJL181W YJL182C MNN11 GON7 YJL185C
MNN5 SWE1
ERG20 SET2 YJL169W ASG7 YJL171C CPS1 RFA3
KRE9 YJL175W SWI3 RPL17B ATG27 PFD1 ATP12
YJL181W YJL182C MNN11 GON7 YJL185C MNN5
TPK1 HAL5 QCR8 ERG20 SET2 YJL169W ASG7
YJL171C CPS1 RFA3 KRE9 YJL175W SWI3 RPL17B
YJL142C TIM17 YJL144W SFH5 IDS2 YJL147C RPA34
YJL149W YJL150W SNA3 YJL152W INO1 VPS35
FBP26 SSY5 YJL156W-A FAR1 CIS3 HSP150 YJL160C
FMP33 JJJ2 YJL163C TPK1 HAL5 QCR8 ERG20 SET2
YJL169W ASG7 YJL171C
URA2 YJL131C YJL132W YJL133C-A MRS3 LCB3
YJL135W RPS21B YJL136W-A GLG2 TIF2 YUR1
RPB4 YAK1 YJL142C TIM17 YJL144W SFH5 IDS2
YJL147C RPA34 YJL149W
NCA3 PHO86 YJL118W YJL119C YJL120W RPE1
YJL122W YJL123C LSM1 GCD14 NIT2 SPT10
YJL127C-B YJL127W-A PBS2 TRK1 URA2 YJL131C
YJL132W YJL133C-A MRS3 LCB3 YJL135W RPS21B
YJL136W-A GLG2 TIF2
YJL113W YJL114W ASF1 NCA3 PHO86 YJL118W
YJL119C YJL120W RPE1 YJL122W YJL123C LSM1
GCD14 NIT2 SPT10
GZF3 CCT7 MDV1 YJL113W YJL114W ASF1 NCA3
GSH1 MEF2 YJL103C PAM16 SET4 IME2 YJL107C
PRM10 UTP10 GZF3 CCT7 MDV1
YJL086C TRL1 ARG3 SIP4 DPB11 GWT1 HPR5 TOK1
KHA1
YJL062W-A MRPL8 YJL064W DLS1 MPM1 YJL067W
YJL068C UTP18 YJL070C ARG2 PSF2 JEM1 SMC3
APQ13
YJL052C-A TDH1 PEP8 TIM54 YJL055W ZAP1
YJL057C BIT61 YHC3 BNA3 NUP82 LAS21 YJL062WA MRPL8
YJL043W GYP6 YJL045W YJL046W RTT101
YJL047C-A UBX6 YJL049W MTR4 YJL051W
YJL052C-A TDH1 PEP8 TIM54 YJL055W ZAP1
YJL057C BIT61
KAR2 TAD2 SNX4 YJL037W YJL038C NUP192 NSP1
838
M10_374040_387
893
10
374040
387893
M10_388461_388
515
10
388461
388515
M10_393255_404
508
10
393255
404508
M10_422538_453
116
10
422538
453116
M10_461201_464
261
10
461201
464261
M10_468983_469
207
10
468983
469207
M10_470292_471
990
10
470292
471990
M10_472146_503
466
10
472146
503466
M10_509429_513
451
10
509429
513451
M10_535311_548
177
10
535311
548177
M10_568228_572
479
10
568228
572479
M10_573371_581
691
10
573371
581691
M10_584276_612
602
10
584276
612602
M10_621762_628
593
10
621762
628593
M10_646911_646
10
646911
646911
MHP1
PET130 APS3 RRN7 YJL026C-A RNR2 YJL027C
YJL028W VPS53 MAD2 BET4 YJL032W HCA4 KAR2
TAD2 SNX4 YJL037W YJL038C NUP192 NSP1
YJL022W PET130 APS3 RRN7 YJL026C-A RNR2
YJL027C YJL028W VPS53 MAD2 BET4 YJL032W
HCA4 KAR2 TAD2 SNX4
RPC17 VTC4 YJL012C-A MAD3 CCT3 YJL015C
YJL016W YJL017W YJL018W MPS3 BBC1 YJL020WA YJL021C YJL022W PET130 APS3 RRN7 YJL026C-A
RNR2 YJL027C YJL028W VPS53 MAD2 BET4
YJL032W HCA4
PRE3 OST1 COX16 SYS1 CYR1 CTK2 YJL007C CCT8
YJL009W YJL010C RPC17 AVT1 MPP10 YJR003C
SAG1 YJR005C-A APL1 HYS2 SUI2 YJR008W TDH2
SPC1 MET3 YJR011C YJR012C GPI14 RBF22
SUI2 YJR008W TDH2 SPC1 MET3 YJR011C YJR012C
GPI14 RBF22 YJR015W ILV3 ESS1 YJR018W TES1
YJR020W REC107 LSM8 YJR023C YJR024C BNA1
YJR026W
YJR012C GPI14 RBF22 YJR015W ILV3 ESS1 YJR018W
TES1 YJR020W REC107 LSM8 YJR023C YJR024C
BNA1 YJR026W YJR027W
GPI14 RBF22 YJR015W ILV3 ESS1 YJR018W TES1
YJR020W REC107 LSM8 YJR023C YJR024C BNA1
YJR026W YJR027W YJR029W
YJR015W ILV3 ESS1 YJR018W TES1 YJR020W
REC107 LSM8 YJR023C YJR024C BNA1 YJR026W
YJR027W YJR029W YJR030C GEA1 CPR7 RAV1
PET191 RAD26 HUL4 YJR037W YJR038C YJR039W
GEF1 URB2
HUL4 YJR037W YJR038C YJR039W GEF1 URB2
NUP85 POL32 VPS55 SSC1 TAH11
CYC1 UTR1 ISY1 OSM1 RAD7 BFA1 YJR054W HIT1
YJR056C CDC8 APS2 PTK2 CBF1 YJR061W NTA1
RPA12 CCT5
ARP3 TOR1 YAE1 RFC2 HAM1 LIA1 YJR071W NPA3
OPI3 MOG1 HOC1 CDC11 MIR1 BNA2 YJR079W
FMP26 EAF6
YAE1 RFC2 HAM1 LIA1 YJR071W NPA3 OPI3 MOG1
HOC1 CDC11 MIR1 BNA2 YJR079W FMP26 EAF6
ACF4 CSN12 YJR085C STE18 YJR087W YJR088C
BIR1
HOC1 CDC11 MIR1 BNA2 YJR079W FMP26 EAF6
ACF4 CSN12 YJR085C STE18 YJR087W YJR088C
BIR1 GRR1 JSN1 BUD4 FIP1 IME1 RPL43B SFC1
YJR096W JJJ3 YJR098C YUH1 YJR100C RSM26
VPS25 URA8
JJJ3 YJR098C YUH1 YJR100C RSM26 VPS25 URA8
SOD1 ADO1 ECM27 YJR107W ABM1 CPA2 YMR1
YJR111C NNF1 YJR112W-A RSM7
NNF1 YJR112W-A RSM7 SRF2 YJR115W YJR116W
911
M10_698149_715
254
10
698149
715254
10
731761
731761
11
590
590
11
9262
18921
11
25990
31187
11
42738
47707
M11_79182_9833
6
11
79182
98336
M11_103658_114
412
11
103658
114412
M11_120696_131
394
11
120696
131394
M11_136397_153
463
11
136397
153463
M11_171771_180
221
11
171771
180221
M11_194611_212
554
11
194611
212554
M11_218377_222
724
11
218377
222724
M11_229040_238
310
11
229040
238310
M11_247944_247
956
11
247944
247956
M11_258243_272
657
11
258243
272657
M11_298361_298
361
11
298361
298361
M11_308932_315
253
11
308932
315253
M10_731761_731
761
M11_590_590
M11_9262_18921
M11_25990_3118
7
M11_42738_4770
7
STE24 ILM1 YJR119C YJR120W ATP2 CAF17 RPS5
YJR124C ENT3
HOM6 HIR3 YJR140W-A YJR141W YJR142W PMT4
MGM101 RPS4A YJR146W HMS2 BAT2 YJR149W
DAN1 DAN4 YJR151W-A DAL5 PGU1
PGU1 YJR154W AAD10 THI11 YJR157W HXT16 SOR1
MPH3
FRE2 MCH2 YKL222C YKL223W YKL224C YKL225W
YKL215C URA1 JEN1 SRY1 COS9 FRE2 MCH2
YKL222C YKL223W YKL224C YKL225W
UBA1 TRP3 SAC1 DOA1 YRA2 YKL215C URA1 JEN1
SRY1
EAP1 LOS1 YKL206C YKL207W CBT1 STE6 UBA1
TRP3 SAC1 DOA1
PRS1 FAS1 YKL183C-A LOT5 SPE1 ASH1 MTR2
YKL187C PXA2 HYM1 CNB1 DPH2 ACP1 SDS22
MST1 MIA40 YKT6 PEX1 PTK1
SNU114 YKL174C ZRT3 LST4 YKL177W STE3 COY1
RPL17A PRS1 FAS1 YKL183C-A LOT5 SPE1 ASH1
MCD4 YKL165C-A TPK3 MRP49 KKQ8 YKL169C
MRPL38 YKL171W EBP2 SNU114 YKL174C ZRT3
LST4 YKL177W STE3 COY1
SRP102 RSM22 YKL156C-A RPS27A APE2 YKL158W
RCN1 ELF1 YKL161C YKL162C YKL162C-A PIR3
PIR1 MCD4 YKL165C-A TPK3 MRP49 KKQ8
YKL169C MRPL38 YKL171W EBP2
APL2 YKL136W YKL137W MRPL31 HSK3 CTK1
TGL1 SDH3 MRP8 LTV1 RPC25 RPT1 YKL145W-A
AVT3 YKL147C SDH1 DBR1 MCR1 YKL151C GPM1
YKL153W SRP102
PRR1 SBA1 YKL118W VPH2 OAC1 YKL121W SRP21
YKL123W SSH4 RRN3 YPK1 PGM1 PMU1 MYO3
SHE2 YKL131W RMA1 YKL133C OCT1 APL2
YKL136W YKL137W MRPL31 HSK3
HAP4 KTI12 YKL111C ABF1 RAD27 APN1 YKL115C
PRR1 SBA1 YKL118W VPH2 OAC1 YKL121W SRP21
YKL123W SSH4 RRN3
YKL102C LAP4 GFA1 YKL105C YKL106C-A AAT1
YKL107W SLD2 HAP4 KTI12 YKL111C ABF1 RAD27
APN1 YKL115C PRR1 SBA1
YKL098W UTP11 YKL100C YKL100W-A HSL1
YKL102C LAP4 GFA1 YKL105C
RRP14 YKL083W HOT13 MDH1 SRX1 CYT2
YKL088W MIF2 CUE2 YKL091C BUD2 MBR1 YJU3
YJU2 YKL096C-B CWP1 CWP2 YKL097C YKL097WA YKL098W UTP11 YKL100C YKL100W-A HSL1
YKL069W YKL070W YKL071W STB6 LHS1 MUD2
YKL075C PSY1 YKL077W DHR2
MSN4 YKL063C MNR2 YET1 YKL066W YNK1
NUP100 YKL068W-A YKL069W YKL070W YKL071W
STB6
M11_354466_354
466
11
354466
354466
M11_379062_382
554
11
379062
382554
M11_388373_397
458
11
388373
397458
11
403418
405226
11
421190
421190
11
442468
446685
11
468771
468771
11
482069
484826
M11_508110_510
933
11
508110
510933
M11_522777_522
777
11
522777
522777
M11_527135_533
477
11
527135
533477
11
540588
540588
YKR051W MRS4 YSR3 DYN1 RHO4 TRM2
11
547558
547558
DYN1 RHO4 TRM2 RPS21A GLG1 TIF1 UTP30
11
547810
547810
DYN1 RHO4 TRM2 RPS21A GLG1 TIF1 UTP30
11
547813
556934
11
566015
566015
M11_574956_579
819
11
574956
579819
M11_586769_599
170
11
586769
599170
11
611765
612781
11
618637
619431
11
623215
623215
M11_403418_405
226
M11_421190_421
190
M11_442468_446
685
M11_468771_468
771
M11_482069_484
826
M11_540588_540
588
M11_547558_547
558
M11_547810_547
810
M11_547813_556
934
M11_566015_566
015
M11_611765_612
781
M11_618637_619
431
M11_623215_623
215
PTM1 NFU1 VPS24 SPC42 PHD1 YKL044W PRI2
DCW1 YKL047W ELM1 CSE4
URA6 PAN3 GPX1 YKL027W TFA1 MAE1 YKL030W
YKL031W IXR1 FMP47 YKL033W-A TUL1 UGP1
YKL036C YKL037W
ATP7 HCS1 YKL018C-A SWD2 RAM2 SPT23 MAK11
CDC16 YKL023W URA6 PAN3 GPX1 YKL027W TFA1
MAE1 YKL030W YKL031W IXR1
URB1 PUT3 ATP7 HCS1 YKL018C-A SWD2 RAM2
SPT23 MAK11 CDC16 YKL023W
SFT1 CAP1 LAC1 MRT4 UFD4 CCE1 PRP40 ARC19
URB1
MET14 DID4 MRP17 YKL003W-A AUR1 BYE1 VPS1
PAP1 OSH6 ECM9 YKR004C-A YKR005C MRPL13
MEH1 RSC4 FOX2
TOF2 YKR011C YKR012C PRY2 YPT52 YKR015C
FMP13 YKR017C YKR018C IRS4 VPS51
YKR017C YKR018C IRS4 VPS51 YKR021W YKR022C
YKR023W DBP7 RPC37 GCN3 FMP50
SET3 GMH1 SPO14 YKR032W YKR033C DAL80
YKR035C DID2 CAF4 SPC34 KAE1 GAP1 YKR040C
YKR041W UTH1
GAP1 YKR040C YKR041W UTH1 YKR043C UIP5
YKR045C PET10 YKR047W NAP1 FMP46 TRK2
YKR051W MRS4
YKR040C YKR041W UTH1 YKR043C UIP5 YKR045C
PET10 YKR047W NAP1 FMP46 TRK2 YKR051W
MRS4 YSR3 DYN1
DYN1 RHO4 TRM2 RPS21A GLG1 TIF1 UTP30 KTR2
TFA2 LAS1 YKR064W FMP18 CCP1
UTP30 KTR2 TFA2 LAS1 YKR064W FMP18 CCP1
GPT2 BET3 MET1 YKR070W DRE2
FMP18 CCP1 GPT2 BET3 MET1 YKR070W DRE2 SIS2
YKR073C YKR074W YKR075C YKR075W-A ECM4
YKR077W YKR078W TRZ1
SIS2 YKR073C YKR074W YKR075C YKR075W-A
ECM4 YKR077W YKR078W TRZ1 MTD1 RPF2
NUP133 DAD2 HBS1 MRPL20 PRP16 OMA1 TVP38
STC1
OMA1 TVP38 STC1 PXL1 SRL3 SRP40 PTR2 RPL40B
MLP1
PXL1 SRL3 SRP40 PTR2 RPL40B MLP1 PCC1
YKR096W
PTR2 RPL40B MLP1 PCC1 YKR096W PCK1
M11_624548_624
548
M11_629611_632
952
M11_643655_643
655
M11_645247_645
247
M11_645253_645
253
M11_645409_645
409
M11_645547_645
547
M11_645577_645
577
M11_645589_645
589
M11_645727_645
727
M11_645998_645
998
M11_646028_646
028
M11_646042_646
042
M11_646049_646
049
M11_646054_646
054
M11_646060_646
060
M11_646065_646
065
M11_646146_646
146
M11_646245_646
245
M11_646285_646
285
M11_646408_646
408
M11_646556_646
556
M11_646820_646
820
M11_647318_647
318
M11_647807_647
807
M11_647868_647
11
624548
624548
PTR2 RPL40B MLP1 PCC1 YKR096W PCK1 UBP11
11
629611
632952
MLP1 PCC1 YKR096W PCK1 UBP11 YKR099C-A
BAS1 SKG1 SIR1
11
643655
643655
UBP11 YKR099C-A BAS1 SKG1 SIR1 FLO10
11
645247
645247
YKR099C-A BAS1 SKG1 SIR1 FLO10 NFT1
11
645253
645253
11
645409
645409
11
645547
645547
11
645577
645577
11
645589
645589
11
645727
645727
11
645998
645998
11
646028
646028
11
646042
646042
11
646049
646049
11
646054
646054
11
646060
646060
11
646065
646065
11
646146
646146
11
646245
646245
11
646285
646285
11
646408
646408
11
646556
646556
11
646820
646820
YKR099C-A SKG1 SIR1 FLO10 NFT1
11
647318
647318
YKR099C-A SKG1 SIR1 FLO10 NFT1 YKR104W
11
647807
647807
11
647868
647868
868
M11_647911_647
911
M11_648010_648
010
M11_648055_648
055
M11_648146_648
146
M11_648221_648
221
M11_648280_648
280
M11_648354_648
354
M11_648430_648
430
M11_648545_648
545
M11_648673_648
673
M11_648742_666
052
11
647911
647911
11
648010
648010
11
648055
648055
11
648146
648146
11
648221
648221
11
648280
648280
11
648354
648354
11
648430
648430
11
648545
648545
11
648673
648673
SKG1 SIR1 FLO10 NFT1 YKR104W
11
648742
666052
M12_19609_2776
5
12
19609
27765
M12_35970_3597
0
12
35970
35970
M12_55040_8636
9
12
55040
86369
12
92674
95639
12
99261
99261
12
108809
126934
12
131338
131338
12
145780
145780
M12_195531_210
539
12
195531
210539
M12_238298_246
579
12
238298
246579
M12_247886_257
512
12
247886
257512
M12_92674_9563
9
M12_99261_9926
1
M12_108809_126
934
M12_131338_131
338
M12_145780_145
780
SKG1 SIR1 FLO10 NFT1 YKR104W YKR105C
YKR106W
AQY2 YLL053C YLL054C YLL055W YLL056C JLP1
YLL058W YLL059C GTT2 MMP1 MHT1 AYT1
YLL064C YLL065W
YBT1 YLL049W COF1 FRE6 AQY2 YLL053C
YLL054C YLL055W YLL056C JLP1
YLL025W HSP104 ISA1 TPO1 YLL029W YLL030C
GPI13 YLL032C YLL033W RIX7 GRC3 PRP19
YLL037W ENT4 UBI4 VPS13 SDH2 ATG10 FPS1
YLL044W RPL8B RNP1 YLL047W
SPA2 HIF1 YLL023C SSA2 YLL025W HSP104 ISA1
TPO1
COX19 KNS1 YLL019W-A YLL020C SPA2 HIF1
YLL023C SSA2 YLL025W HSP104
YLL006W-A YLL007C DRS1 COX17 PSR1 SOF1 YEH1
PUF3 YLL014W BPT1 YLL016W YLL017W DPS1
COX19 KNS1 YLL019W-A YLL020C SPA2 HIF1
SPO75 MMM1 YLL006W-A YLL007C DRS1 COX17
PSR1 SOF1 YEH1 PUF3 YLL014W
DNM1 RTT109 SFI1 ORC3 SPO75 MMM1 YLL006W-A
YLR001C NOC3
IZH3 UBR2 SNF7 SED5 AAT2 ADE16 RPL15A
YLR030W YLR031W RAD5 RSC58 SMF3 MLH2
YLR035C-A
YLR040C YLR041W YLR042C TRX1 PDC1 STU2
YLR046C YLR047C RPS0B YLR049C YLR050C
YLR051C IES3 YLR053C OSW2 SPT8 ERG3
YLR046C YLR047C RPS0B YLR049C YLR050C
YLR051C IES3 YLR053C OSW2 SPT8 ERG3 YLR057W
M12_260113_260
119
12
260113
260119
M12_264911_282
091
12
264911
282091
M12_282397_292
529
12
282397
292529
12
317542
321827
12
326212
332574
M12_370434_381
903
12
370434
381903
M12_388933_388
933
12
388933
388933
12
423789
423789
12
433955
433958
M12_450041_508
029
12
450041
508029
M12_514835_516
700
12
514835
516700
M12_553064_556
063
12
553064
556063
12
570433
570433
12
582499
582499
12
607076
607076
M12_611810_611
997
12
611810
611997
M12_634225_635
380
12
634225
635380
M12_317542_321
827
M12_326212_332
574
M12_423789_423
789
M12_433955_433
958
M12_570433_570
433
M12_582499_582
499
M12_607076_607
076
SHM2 REX2 FRS1 RPL22A BUD28 YLR063W
YLR064W YLR065C SPC3
SPT8 ERG3 YLR057W SHM2 REX2 FRS1 RPL22A
BUD28 YLR063W YLR064W YLR065C SPC3 PET309
YLR057W SHM2 REX2 FRS1 RPL22A BUD28
YLR063W YLR064W YLR065C SPC3 PET309 FYV7
MEF1 XYL2 RGR1 YLR072W YLR073C BUD20 RPL10
YLR076C FMP25 BOS1 SIC1 EMP46 GAL2
MEF1 XYL2 RGR1 YLR072W YLR073C BUD20 RPL10
YLR076C FMP25 BOS1 SIC1 EMP46 GAL2 SRL2
EMP70 RAX2 ARP6
CSF1 GAA1 ALT1 XDJ1 YLR091W SUL2 NYV1 GIS3
IOC2
GAA1 ALT1 XDJ1 YLR091W SUL2 NYV1 GIS3 IOC2
KIN2 HRT3 CHA4 ICT1 YLR099W-A ERG27
REX3 YLR108C AHP1 CCW12 YLR111W YLR112W
HOG1 YLR114C CFT2 MSL5 CLF1 YLR118C SRN2
YPS1 YLR120W-A YPS3 YLR122C YLR123C
YLR124W
CFT2 MSL5 CLF1 YLR118C SRN2 YPS1 YLR120W-A
YPS3 YLR122C YLR123C YLR124W YLR125W
YLR126C APC2
SLX4 TIS11 YLR137W NHA1 SLS1 YLR140W RRN5
PUT1 YLR143W ACF2 RMP1 SPE4
RRN5 PUT1 YLR143W ACF2 RMP1 SPE4 SMD3 PEP3
YLR149C YLR149C-A STM1 PCD1 YLR152C
YLR149C-A STM1 PCD1 YLR152C ACS2 RNH203
YLR154C-G YLR154C-H TAR1 YLR154W-B
YLR154W-C YLR154W-E YLR154W-F ASP3-1
YLR156C-A YLR156W ASP3-2 YLR157C-C YLR157WA YLR157W-C ASP3-3 YLR159C-A YLR159W ASP3-4
YLR161W YLR162W YLR162W-A YLR162W- MAS1
YLR163W-A YLR164W PUS5 SEC10 RPS31 YLR168C
YLR169W APS1 YLR171W DPH5 YLR173W IDP2
CBF5 RFX1 YLR177W TFS1 YLR179C SAM1 VTA1
IDP2 CBF5 RFX1 YLR177W TFS1 YLR179C SAM1
VTA1 SWI6 TOS4 YLR184W RPL37A EMG1 SKG3
PWP1 SIK1 YLR198C YLR199C YKE2 FMP53
YLR202C MSS51 QRI5 HMX1 ENT2 HRD3 SEC13
PNP1 CLB4 YLR211C TUB4
PNP1 CLB4 YLR211C TUB4 CRR1 FRE1 CDC123
CPR6 YLR217W YLR218C MSC3 CCC1 RSA3
CPR6 YLR217W YLR218C MSC3 CCC1 RSA3 UTP13
YLR222C-A IFH1 YLR224W YLR225C BUR2 ADY4
ECM22 CDC42 YLR230W BNA5 YLR232W EST1
TOP3 YLR235C YLR236C THI7 FAR10 LIP2
CDC42 YLR230W BNA5 YLR232W EST1 TOP3
YLR235C YLR236C THI7 FAR10 LIP2 VPS34
YLR241W
YLR243W MAP1 CDD1 ERF2 YLR247C RCK2 YEF3
SSP120 SYM1 YLR252W YLR253W NDL1
M12_642137_644
136
12
642137
644136
M12_659357_674
651
12
659357
674651
M12_677957_697
260
12
677957
697260
M12_704828_708
594
12
704828
708594
M12_710924_719
857
12
710924
719857
M12_721979_744
436
12
721979
744436
M12_748567_757
807
12
748567
757807
M12_759664_777
813
12
759664
777813
M12_782839_790
025
12
782839
790025
M12_796771_815
552
12
796771
815552
M12_824230_824
230
12
824230
824230
M12_829265_829
705
12
829265
829705
M12_849485_855
776
12
849485
855776
M12_858996_872
460
12
858996
872460
M12_881579_881
903
12
881579
881903
RCK2 YEF3 SSP120 SYM1 YLR252W YLR253W NDL1
YLR255C HAP1
YLR257W GSY2 HSP60 LCB5 VPS63 YPT6 RBF7
RED1 YLR264C-A RPS28B NEJ1 PDR8 BOP2 SEC22
YLR269C DCS1 YLR271W
VPS63 YPT6 RBF7 RED1 YLR264C-A RPS28B NEJ1
PDR8 BOP2 SEC22 YLR269C DCS1 YLR271W YCS4
PIG1 CDC46 SMD2 DBP9 YSH1 YLR278C YLR279W
YLR280C YLR281C YLR282C YLR283W ECI1
DBP9 YSH1 YLR278C YLR279W YLR280C YLR281C
YLR282C YLR283W ECI1 YLR285C-A NNT1 CTS1
YLR286W-A YLR287C RPS30A MEC3 GUF1 YLR290C
YLR278C YLR279W YLR280C YLR281C YLR282C
YLR283W ECI1 YLR285C-A NNT1 CTS1 YLR286W-A
YLR287C RPS30A MEC3 GUF1 YLR290C GCD7
SEC72 GSP1 YLR294C ATP14 YLR296W YLR297W
YHC1 YLR299C-A ECM38 EXG1
RPS30A MEC3 GUF1 YLR290C GCD7 SEC72 GSP1
YLR294C ATP14 YLR296W YLR297W YHC1
YLR299C-A ECM38 EXG1 YLR301W YLR302C
MET17 ACO1 STT4 UBC12 YLR307C-A CDA1 CDA2
IMH1
STT4 UBC12 YLR307C-A CDA1 CDA2 IMH1 CDC25
YLR311C YLR312C YLR312C-B MRPL15 SPH1 CDC3
NKP2 TAD3 YLR317W
IMH1 CDC25 YLR311C YLR312C YLR312C-B
MRPL15 SPH1 CDC3 NKP2 TAD3 YLR317W EST2
BUD6 MMS22 SFH1 VPS65 CWC24 PEX30 RPL38
YLR326W RBF9 NMA1 REC102
MMS22 SFH1 VPS65 CWC24 PEX30 RPL38 YLR326W
RBF9 NMA1 REC102 CHS5 JIP3 MID2 RPS25B
YLR334C NUP2
REC102 CHS5 JIP3 MID2 RPS25B YLR334C NUP2
SGD1 VRP1 YLR338W YLR339C RPP0 SPO77 FKS1
YLR342W-A GAS2 RPL26A YLR345W YLR346C
KAP95 YLR347W-A
YLR342W-A GAS2 RPL26A YLR345W YLR346C
KAP95 YLR347W-A DIC1 YLR349W ORM2 NIT3
YLR352W
RPL26A YLR345W YLR346C KAP95 YLR347W-A
DIC1 YLR349W ORM2 NIT3 YLR352W BUD8 TAL1
ILV5
YLR356W RSC2 YLR358C ADE13 VPS38 DCR2
YLR361C-A STE11 NMD4 YLR363W-A YLR364C-A
YLR364W YLR365W YLR366W RPS22B MDM30
SSQ1 ARC18 ROM2
YLR361C-A STE11 NMD4 YLR363W-A YLR364C-A
YLR364W YLR365W YLR366W RPS22B MDM30
SSQ1 ARC18 ROM2 SUR4 VID22 YLR374C STP3
PSY3 FBP1 SEC61 YLR379W CSR1 CTF3
YLR374C STP3 PSY3 FBP1 SEC61 YLR379W CSR1
CTF3 NAM2 RHC18 IKI3
M12_899898_927
421
12
899898
927421
M12_956366_964
989
12
956366
964989
M12_965218_987
750
12
965218
987750
12
990751
12
100671
1
100055
4
100671
1
12
101401
6
103950
1
104207
2
105609
7
105980
6
106708
5
105430
2
105610
3
105993
0
106712
3
M12_990751_100
0554
M12_1006711_10
06711
M12_1014016_10
39501
M12_1042072_10
54302
M12_1056097_10
56103
M12_1059806_10
59930
M12_1067085_10
67123
12
12
12
12
M13_27644_2869
4
13
27644
28694
M13_33501_3368
1
13
33501
33681
M13_46070_6912
2
13
46070
69122
M13_77684_8135
8
13
77684
81358
M13_87587_1000
48
13
87587
100048
M13_110808_130
069
13
110808
130069
M13_149075_159
533
13
149075
159533
M13_163180_164
13
163180
164026
IKI3 SWC7 VAC14 REH1 RPS29A STE23 ECM19
CCW14 YLR391W-A YLR392C ATP10 CST9 COX8
VPS33 AFG2 SKI2 BDF1 YLR399W-A YLR400W DUS3
YLR402W SFP1 YLR404W DUS4 RPL31B YLR406C-A
YLR407W YLR408C UTP21
CTR3 YLR412C-A YLR412W YLR413W YLR414C
YLR415C YLR416C VPS36 CDC73 YLR419W URA4
RPN13 YLR422W ATG17 SPP382
VPS36 CDC73 YLR419W URA4 RPN13 YLR422W
ATG17 SPP382 TUS1 YLR426W MAG2 YLR428C
CRN1 SEN1
TUS1 YLR426W MAG2 YLR428C CRN1 SEN1 ATG23
IMD3 CNA1 YLR434C TSR2 ECM30
SEN1 ATG23 IMD3 CNA1 YLR434C TSR2 ECM30
YLR437C YLR437C-A LSM3 CAR2 MRPL4 SEC39
CNA1 YLR434C TSR2 ECM30 YLR437C YLR437C-A
LSM3 CAR2 MRPL4 SEC39 RPS1A SIR3 ECM7
YLR444C YLR445W YLR446W VMA6 RPL6B FPR4
HMG2 LEU3 SST2 RIF2 FMP27
HMG2 LEU3 SST2 RIF2 FMP27 YLR455W YLR456W
NBP1 YLR458W GAB1 YLR460C PAU4
FMP27 YLR455W YLR456W NBP1 YLR458W GAB1
YLR460C PAU4
YLR455W YLR456W NBP1 YLR458W GAB1 YLR460C
PAU4 YLR462W YLR463C YLR464W BSC3 YRF1-4
GAB1 YLR460C PAU4 YLR462W YLR463C YLR464W
BSC3 YLR466C-A YLR466C-B YRF1-4 YRF1-5
YML116W-A NAB6 YML117W-A NGL3 YML119W
NDI1 GTR1 YML122C PHO84 TUB3 YML125C ERG13
RSC9
TAF8 VAN1 ATR1 YML116W-A NAB6 YML117W-A
NGL3 YML119W NDI1 GTR1 YML122C PHO84
VPS9 TAF13 ARG81 YML099W-A TSL1 YML100W-A
CUE4 YML101C-A YML102C-A CAC2 NUP188 MDM1
SEC65 URA5 YML107C YML108W ZDS2 COQ5 BUL2
CTK3 DAT1 TAF8 VAN1 ATR1 YML116W-A
YML117W-A
YML089C YML090W RPM2 PRE8 UTP14 YML094C-A
GIM5 RAD10 YML096W VPS9 TAF13 ARG81
YML099W-A TSL1 YML100W-A CUE4 YML101C-A
YML102C-A CAC2
DUS1 ATP18 YML081W YML082W YML083C
YML084W TUB1 ALO1 YML087C UFO1 YML089C
YML090W RPM2 PRE8 UTP14 YML094C-A GIM5
RAD10 YML096W VPS9
ERV41 ITT1 POB3 DAK1 COG8 TCB3 RPL6A FPR3
HMG1 WAR1 BET5 CPR3 YML079W DUS1 ATP18
YML081W YML082W
YML053C CYB2 YML054C-A SPC2 IMD4 YML057C-A
CMP2 SML1 HUG1 NTE1 OGG1 PIF1 MFT1 RPS1B
TEM1 ORC1 SMA2 ERV41
YML050W GAL80 SUR7 YML053C CYB2 YML054C-A
026
M13_178636_203
101
13
178636
203101
M13_205921_205
921
13
205921
205921
M13_216022_216
028
13
216022
216028
M13_227254_243
624
13
227254
243624
M13_245457_255
564
13
245457
255564
M13_261719_286
122
13
261719
286122
M13_298181_299
950
13
298181
299950
M13_328865_328
865
13
328865
328865
M13_361370_362
346
13
361370
362346
M13_371857_379
981
13
371857
379981
M13_390351_403
766
13
390351
403766
M13_404546_404
546
13
404546
404546
M13_410287_430
164
13
410287
430164
M13_437167_445
622
13
437167
445622
M13_480708_507
291
13
480708
507291
SPC2 IMD4 YML057C-A CMP2 SML1 HUG1 NTE1
YML033W YML034C-A SRC1 AMD1 YML035C-A
YML036W YML037C YMD8 YML039W YML040W
VPS71 CAT2 RRN11 YML045W PRP39 PRM6
YML047W-A GSF2 YML048W-A RSE1 YML050W
GAL80 SUR7 YML053C
YML031C-A NDC1 RAD52 YML032C-A YML033W
YML034C-A SRC1 AMD1 YML035C-A YML036W
YML037C YMD8 YML039W YML040W
YML6 RPS18B YOX1 TSA1 USA1 YML030W
YML031C-A NDC1 RAD52 YML032C-A YML033W
YML034C-A SRC1 AMD1 YML035C-A
YML007C-A ERG6 MRPL39 YML009C-A YML009W-B
SPT5 YML010W-A YML010C-B YML010W-B
YML011C YML012C-A ERV25 SEL1 YML013C-A
TRM9 TAF11 PPZ1 PSP2 YML018C OST6 YML020W
UNG1 APT1 YML023C RPS17A YML6 RPS18B YOX1
TSA1 USA1
YML003W GLO1 TRM12 GIS4 YML007C-A YAP1
ERG6 MRPL39 YML009C-A YML009W-B SPT5
YML010W-A YML010C-B YML010W-B YML011C
YML012C-A ERV25 SEL1 YML013C-A TRM9 TAF11
PPZ1 PSP2
YPT7 YML002W YML003W GLO1 TRM12 GIS4
YML007C-A YAP1 ERG6 CDC5 YMR001C-A
YMR002W YMR003W MVP1 TAF4 PLB2 YMR007W
PLB1 YMR009W YMR010W HXT2 CLU1 SEC59
HXT2 CLU1 SEC59 YMR013C-A YMR013W-A BUD22
ERG5 SOK2 SPO20
QRI8 MSS1 MRPL3 CSI1 PEX12 YMR027W TAP42
FAR8 RSF1 YMR030W-A YMR031C YMR031W-A
HOF1 ARP9
YMR041C ARG80 MCM1 IOC4 YMR045C YMR046C
YMR046W-A NUP116 CSM3 ERB1
YMR046C YMR046W-A NUP116 CSM3 ERB1
YMR050C YMR052C-A FAR3 STB2 STV1 BUB2 AAC1
YMR057C FET3
STB2 STV1 BUB2 AAC1 YMR057C FET3 SEN15
SAM37 RNA14 ECM40 RIM9 AEP1 KAR5 SOV1 UBX4
AVO2 NAT4 MOT3 TVP18 ABF2 YMR073C YMR074C
ECM40 RIM9 AEP1 KAR5 SOV1 UBX4 AVO2 NAT4
MOT3 TVP18 ABF2 YMR073C YMR074C
KAR5 SOV1 UBX4 AVO2 NAT4 MOT3 TVP18 ABF2
YMR073C YMR074C YMR075C-A RCO1 PDS5 VPS20
CTF18 SEC14 NAM7 ISF1 YMR082C ADH3 YMR084W
YMR085W
NAM7 ISF1 YMR082C ADH3 YMR084W YMR085W
YMR086C-A YMR086W YMR087W YMR088C YTA12
YMR090W NPL6 AIP1 UTP15
YMR102C YMR103C YPK2 PGM2 YMR105W-A
YKU80 SPG4 ILV2 MYO5 YMR110C YMR111C
MED11 FOL3 YMR114C FMP24 ASC1 SPC24
M13_507299_508
627
13
507299
508627
13
513778
513778
13
535359
535359
M13_554836_562
907
13
554836
562907
M13_564142_574
867
13
564142
574867
13
597705
597711
13
649250
649253
13
686206
686206
13
697899
698980
13
718930
727057
13
789460
789466
13
824809
824809
13
843356
843356
13
843590
843590
M13_846240_850
520
13
846240
850520
M13_855629_855
635
13
855629
855635
M13_885665_885
665
13
885665
885665
M13_905780_922
268
13
905780
922268
13
923511
923511
14
13845
13845
M13_513778_513
778
M13_535359_535
359
M13_597705_597
711
M13_649250_649
253
M13_686206_686
206
M13_697899_698
980
M13_718930_727
057
M13_789460_789
466
M13_824809_824
809
M13_843356_843
356
M13_843590_843
590
M13_923511_923
511
M14_13845_1384
YMR118C ASI1 YMR119W-A ADE17 RPL15B
YMR122C YMR122W-A PKR1 YMR124W
FMP24 ASC1 SPC24 YMR118C ASI1 YMR119W-A
ADE17 RPL15B YMR122C YMR122W-A PKR1
YMR124W
ASI1 YMR119W-A ADE17 RPL15B YMR122C
YMR122W-A PKR1 YMR124W STO1 DLT1 SAS2
ECM16 POM152 YMR130W RRB1 JLP2 REC114
YMR134W GID8 YMR135W-A GAT2 PSO2
CIN4 RIM11 SIP5 YMR141C YMR141W-A RPL13B
RPS16A YMR144W NDE1 TIF34 YMR147W
YMR148W SWP1 IMP1 YIM2 YIM1 YMR153C-A
NUP53 RIM13 YMR155W TPP1 FMP39 MRPS8
NDE1 TIF34 YMR147W YMR148W SWP1 IMP1 YIM2
YIM1 YMR153C-A NUP53 RIM13 YMR155W TPP1
FMP39 YMR158C-A YMR158C-B YMR158W-A
MRPS8 YMR158W-B ATG16 YMR160W HLJ1 DNF3
MSS11 SMP2 YMR166C MLH1 CEP3 ALD3 ALD2
YMR171C HOT1
SGS1 SPG5 GYL1 YMR193C-A MRPL24 YMR194C-A
YMR194C-B RPL36A ICY1 YMR196W VTI1
YMR206W HFA1 ERG12 YMR209C YMR210W DML1
EFR3 CEF1 SCJ1
YMR210W DML1 EFR3 CEF1 SCJ1 GAS3 SKY1 GUA1
TRS130
ESC1 ERG8 FMP42 FSH2 UBP8 MRE11 MRPL44
YMR226C TAF7 MTF1 RRP5 RPS10B YMR230W-A
PEP5
PET111 YMR258C YMR259C TIF11 TPS3 YMR262W
SAP30 CUE1 YMR265C
RCE1 BUL1 DSK2 FCP1 YMR278W YMR279C CAT8
GPI12 AEP2
AEP2 RIT1 YKU70 NGL2 MRPL33 MSU1 HSH155
ABZ2 HAS1 YMR290W-A
AEP2 RIT1 YKU70 NGL2 MRPL33 MSU1 HSH155
ABZ2 HAS1 YMR290W-A YMR291W
YKU70 NGL2 MRPL33 MSU1 HSH155 ABZ2 HAS1
YMR290W-A YMR291W GOT1 YMR293C JNM1
YMR294W-A YMR295C LCB1
HSH155 ABZ2 HAS1 YMR290W-A YMR291W GOT1
YMR293C JNM1 YMR294W-A YMR295C LCB1 PRC1
YMR298W DYN3
YML058C-A YMR304C-A UBP15 SCW10 YMR306C-A
FKS3 YMR307C-A GAS1 PSE1 NIP1
YMR310C GLC8 ELP6 TGL3 PRE5 YMR315W
YMR315W-A YMR316C-A YMR316C-B DIA1
YMR317W ADH6 FET4 YMR320W YMR321C SNO4
ERR3 YMR324C YMR325W YMR326C
FET4 YMR320W YMR321C SNO4 ERR3 YMR324C
YMR325W YMR326C
MDJ2 PEX6 RPD3 AAD14 THI12 SNZ2 SNO2
5
M14_19885_3885
2
14
19885
38852
M14_61469_6146
9
14
61469
61469
M14_89161_1047
98
14
89161
104798
M14_109527_116
131
14
109527
116131
14
168128
171103
14
191183
191243
14
206186
209852
14
220948
220948
M14_235423_254
155
14
235423
254155
M14_258590_281
187
14
258590
281187
M14_314883_330
368
14
314883
330368
M14_340077_340
077
14
340077
340077
M14_358641_368
178
14
358641
368178
M14_371953_394
161
14
371953
394161
M14_402312_412
269
14
402312
412269
M14_412272_418
269
14
412272
418269
M14_449639_449
14
449639
449639
M14_168128_171
103
M14_191183_191
243
M14_206186_209
852
M14_220948_220
948
YNL335W COS1 YNL337W YNL338W
RFA2 YNL313C DAL82 ATP11 PHA2 PFS2 HXT14
YNL319W YNL320W YNL321W KRE1 LEM3
YNL324W FIG4 PFA3 EGT2 MDJ2 PEX6 RPD3 AAD14
THI12 SNZ2 SNO2 YNL335W
CLA4 TRF5 YNL300W RPL18B RPS19B YNL303W
YPT11 YNL305C MRPS18 MCK1 KRI1 STB1 ZIM17
PRM1 ERG24 HCH1 POP3 WSC2 MRPL10 YNL285W
CUS2 SEC21 CAF40 PCL1 RFC3 MID1 PUS4 MSB3
RIM21
TOF1 YNL274C YNL275W YNL276C MET2
YNL277W-A CAF120 PRM1 ERG24 HCH1 POP3 WSC2
MRPL10
MPA43 RAD50 NRD1 MRPL17 TEX1 YNL254C GIS2
FOL1 SIP3 DSL1
NAR1 ZWF1 ATG2 SLA2 SUI1 CWC25 VPS75
YNL247W RPA49
URE2 ELA1 PDR16 CSL4 BNI4 YNL234W YNL235C
SIN4 YTP1 KEX2 LAP3 NAR1 ZWF1
SSU72 ATG4 YNL224C CNM67 YNL226W JJJ1
YNL228W URE2 ELA1 PDR16 CSL4 BNI4
YNL200C PSY2 SPS19 YNL203C SPS18 YNL205C
RTT106 RIO2 YNL208W SSB2 MER1 YNL211C VID27
YNL213C PEX17 IES2 RAP1 YNL217W MGS1 ALG9
ADE12 POP1 SSU72 ATG4 YNL224C
UBP10 YNL187W KAR1 SRP1 YNL190W YNL191W
CHS1 YNL193W YNL194C YNL195C YNL196C WHI3
YNL198C GCR2 YNL200C PSY2 SPS19 YNL203C
SPS18 YNL205C RTT106 RIO2 YNL208W SSB2 MER1
YNL211C VID27
YNL158W ASI2 YGP1 CBK1 RPL42A YNL162W-A
RIA1 IBD2 YNL165W BNI5 SKO1 FMP41 PSD1
YNL170W YNL171C APC1 MDG1 YNL174W NOP13
YNL176C
YNL149C YNL150W RPC31 YNL152W GIM3 YCK2
YNL155W NSG2 YNL157W YNL158W ASI2 YGP1
CBK1 RPL42A YNL162W-A
KRE33 FYV6 YNL134C FPR1 EAF7 NAM9 SRV2
RCP10 RLR1 YNL140C AAH1 MEP2 YNL143C
YNL144C YNL144W-A MFA2 YNL146C-A YNL146W
LSM7 ALF1 YNL149C YNL150W
DCP2 NCS2 YNL120C TOM70 YNL122C YNL123W
NAF1 ESBP6 SPC98 FAR11 TEP1 NRK1 CPT1
YNL130C-A TOM22 KRE33 FYV6 YNL134C FPR1
EAF7 NAM9 SRV2 RCP10 RLR1
YAF9 YNL108C YNL109W NOP15 CYB5 DBP2 RPC19
YNL114C YNL115C DMA2 MLS1 DCP2 NCS2
YNL120C TOM70 YNL122C YNL123W NAF1
YNL103W-A LEU4 YNL105W INP52 YAF9 YNL108C
YNL109W NOP15 CYB5 DBP2 RPC19 YNL114C
YNL115C DMA2 MLS1 DCP2
YNL089C RHO2 NST1 YNL092W YPT53 APP1
639
M14_486861_486
861
14
486861
486861
M14_502316_525
064
14
502316
525064
M14_534449_542
648
14
534449
542648
M14_547071_568
748
14
547071
568748
M14_571885_595
885
14
571885
595885
14
614342
618548
14
648788
648788
14
686853
689939
M14_690372_695
114
14
690372
695114
M14_701565_714
215
14
701565
714215
M14_731633_732
029
14
731633
732029
M14_614342_618
548
M14_648788_648
788
M14_686853_689
939
M15_1152_43217
15
1152
43217
15
44482
44550
15
47951
54769
M15_59733_7672
4
15
59733
76724
M15_89211_1062
72
15
89211
106272
M15_108577_154
15
108577
154309
M15_44482_4455
0
M15_47951_5476
9
YNL095C RPS7B PHO23 YNL097C-A YNL097W-A
RAS2
RPL16B TOM7 LAT1 RNH201 MSK1 MLF3 IMP4
MKS1 APJ1 NIS1 TPM1 YNL080C
YNL050C COG5 COX5A MSG5 VAC7 POR1
YNL056W YNL057W YNL058C ARP5 NOP2 GCD10
MTQ1 YDJ1 AQR1 SUN4 RPL9B YNL067W-A
YNL067W-B FKH2 RPL16B TOM7
COG6 BOP3 YNL042W-B YNL043C YIP3 YNL045W
YNL046W SLM2 ALG11 SFB2 YNL050C COG5
COX5A MSG5 VAC7
KTR5 HHF2 HHT2 SIW14 YNL033W YNL034W
YNL035C NCE103 IDH1 GPI15 BDP1 YNL040W COG6
BOP3 YNL042W-B YNL043C YIP3 YNL045W
YNL046W SLM2 ALG11
PBI2 PUB1 YNL017C YNL018C YNL019C ARK1
HDA1 YNL022C FAP1 YNL024C YNL024C-A SSN8
SAM50 CRZ1 YNL028W KTR5 HHF2 HHT2 SIW14
YNL033W YNL034W YNL035C
DOM34 RLP7 PET8 HRB1 MRP7 LST8 SIS1 ASI3 IDP3
YNL010W YNL011C SPO1 YNL013C HEF3 PBI2
ATG3 LRO1 YNR009W CSE2 PRP2 URK1 PHO91
YNR014W SMM1 ACC1
YNR029C ECM39 SSK2 HUB1 PPG1 ABZ1 SOL1
YNR034W-A ARC35 YNR036C RSM19 DBP6 ZRG17
SSK2 HUB1 PPG1 ABZ1 SOL1 YNR034W-A ARC35
YNR036C RSM19 DBP6 ZRG17 YNR040W COQ2
YNR042W MVD1 AGA1
YNR034W-A ARC35 YNR036C RSM19 DBP6 ZRG17
YNR040W COQ2 YNR042W MVD1 AGA1 PET494
YNR046W YNR047W YNR048W MSO1 LYS9 BRE5
POP2 NOG2 ESF2
NOG2 ESF2 HOL1 BIO5 BIO4 BIO3 MNT4 FRE4
CTR9 PSF3 PEX11 SPT20 DCP1 YOL150C GRE2 FRE7
YOL153C ZPS1 YOL155C YOL155W-A HXT11
YOL157C ENB1 YOL159C YOL159C-A YOL160W
YOL161C YOL162W YOL163W YOL164W YOL164WA AAD15 YOL166C YOL166W-A
NOP8 CTR9 PSF3 PEX11 SPT20 DCP1 YOL150C GRE2
FRE7 YOL153C ZPS1
YOL138C CDC33 ARG8 PPM2 RRP40 RIB4 NOP8
CTR9 PSF3 PEX11 SPT20 DCP1 YOL150C GRE2 FRE7
YOL124C YOL125W MDH2 RPL25 YGK3 VPS68
ALR1 YOL131W GAS4 HRT1 YOL134C MED7 PFK27
BSC6 YOL138C CDC33 ARG8 PPM2 RRP40 RIB4
NOP8 CTR9
WSC3 YOL106W YOL107W INO4 ZEO1 SHR5
YOL111C MSB4 SKM1 YOL114C TRF4 MSN1 RRI2
YOL118C MCH4 RPL18A RPS19A SMF1 HRP1
YOL124C YOL125W MDH2 RPL25
PHM7 YOL085C YOL085W-A ADH1 YOL086W-A
309
M15_170945_180
961
15
170945
180961
M15_193911_193
911
15
193911
193911
M15_202370_210
839
15
202370
210839
M15_220337_220
337
15
220337
220337
M15_248746_248
746
15
248746
248746
M15_255000_255
015
15
255000
255015
M15_272023_276
475
15
272023
276475
M15_277470_282
525
15
277470
282525
M15_290670_301
077
15
290670
301077
M15_338018_348
934
15
338018
348934
M15_357032_407
690
15
357032
407690
M15_409775_439
041
15
409775
439041
M15_445656_446
514
15
445656
446514
M15_461652_461
694
15
461652
461694
M15_469463_476
328
15
469463
476328
YOL087C MPD2 HAL9 MSH2 SPO21 YOL092W
TRM10 RFC4 HMI1 COQ3 WRS1 YOL097W-A
YOL098C YOL099C PKH2 IZH4 TPT1 ITR2 NDJ1
WSC3 YOL106W YOL107W INO4 ZEO1 SHR5
YOL111C MSB4 SKM1 YOL114C TRF4 MSN1
MDM20 BRX1 ATP19 AVO1 YOL079W REX4 IRA2
ATG19 YOL083C-A YOL083W PHM7 YOL085C
YOL085W-A
RIB2 RTG1 HST1 NUF2 YOL070C EMI5 THP1
YOL073C YOL075C MDM20 BRX1 ATP19
ARG1 GPD2 MAM3 PRS5 APM4 HUS1 MET22 INP54
RIB2 RTG1 HST1 NUF2 YOL070C EMI5 THP1
YOL073C
PSH1 THI20 GPM3 YOL057W ARG1 GPD2 MAM3
PRS5 APM4
YOL036W YOL037C YOL038C-A PRE6 RPP2A RPS15
NOP12 NGL1 NTG2 PEX15 PSK2 YOL046C YOL047C
YOL048C GSH2
MSE1 SMC5 YOL035C YOL036W YOL037C
YOL038C-A PRE6 RPP2A RPS15 NOP12 NGL1 NTG2
PEX15 PSK2
DIS3 YOL022C IFM1 YOL024W LAG2 MIM1 MDM38
YAP7 YOL029C GAS5 SIL1 YOL032W MSE1
TLG2 YOL019W YOL019W-A TAT2 DIS3 YOL022C
IFM1 YOL024W LAG2 MIM1 MDM38 YAP7 YOL029C
GAS5
YOL008W MDM12 RCL1 PLB3 HTZ1 HRD1
YOL013W-A YOL013W-B YOL014W YOL015W CMK2
ESC8 TLG2 YOL019W YOL019W-A TAT2 DIS3
YOL022C
ALG6 YSP3 YOR004W DNL4 YOR006C SGT2 SLG1
YOR008C-A YOR008W-B TIR4 TIR2 AUS1 YOR011WA YOR012W YOR013W RTS1
AUS1 YOR011W-A YOR012W YOR013W RTS1
YOR015W ERP4 PET127 ROD1 YOR019W HSP10
YOR020W-A YOR021C YOR022C AHC1 YOR024W
HST3 BUB3 STI1 CIN5 YOR029W DFG16 CRS5 HMS1
YOR032W-A EXO1 AKR2 YOR034C-A SHE4 PEP12
CYC2 HIR2 CKB2 GLO4 SRF5 CUE5 WHI2 YOR044W
TOM6 DBP5 STD1
PEP12 CYC2 HIR2 CKB2 GLO4 SRF5 CUE5 WHI2
YOR044W TOM6 DBP5 STD1 RAT1 RSB1 YOR050C
YOR051C YOR052C YOR053W VHS3 YOR055W
NOB1 SGT1 ASE1 YOR059C YOR060C CKA2
YOR062C RPL3 YNG1 CYT1
YOR059C YOR060C CKA2 YOR062C RPL3 YNG1
CYT1 YOR066W ALG8 VAM10 VPS5
ALG8 VAM10 VPS5 GYP1 YOR071C YOR072W
YOR072W-A YOR072W-B SGO1 YOR073W-A CDC21
UFE1 SKI7
YOR071C YOR072W YOR072W-A YOR072W-B SGO1
YOR073W-A CDC21 UFE1 SKI7 RTS2 BUD21 ATX2
M15_481586_481
586
M15_488274_491
190
M15_496730_496
730
15
481586
481586
15
488274
491190
15
496730
496730
M15_515917_546
197
15
515917
546197
M15_551819_563
943
15
551819
563943
M15_571103_581
277
15
571103
581277
M15_587256_619
862
15
587256
619862
15
632882
632894
15
683301
690367
M15_703769_715
809
15
703769
715809
M15_747543_747
543
15
747543
747543
M15_779974_798
209
15
779974
798209
M15_802724_819
015
15
802724
819015
M15_838599_850
119
15
838599
850119
M15_854265_880
786
15
854265
880786
M15_889464_889
464
15
889464
889464
M15_632882_632
894
M15_683301_690
367
DIA2 STC2 YOR082C WHI5 YOR084W OST3 TCB1
RTS2 BUD21 ATX2 DIA2 STC2 YOR082C WHI5
YOR084W OST3 TCB1 YVC1 YOR088W VPS21
YOR082C WHI5 YOR084W OST3 TCB1 YVC1
YOR088W VPS21 PTC5 RBF46 ECM3 YOR093C
YVC1 YOR088W VPS21 PTC5 RBF46 ECM3 YOR093C
ARF3 RKI1 RPS7A
RPS7A YOR097C NUP1 KTR1 CRC1 RAS1 YOR102W
OST2 PIN2 YOR105W VAM3 RGS2 YOR108C-A LEU9
INP53 TFC7 YOR111W YOR112W AZF1 YOR114W
TRS33 RPO31 RPT5 YOR118W RIO1 GCY1 YOR121C
PFY1 LEO1
RPO31 RPT5 YOR118W RIO1 GCY1 YOR121C PFY1
LEO1 UBP2 CAT5 IAH1 RGA1 ADE2 YOR129C ORT1
YOR131C
RGA1 ADE2 YOR129C ORT1 YOR131C VPS17 EFT1
BAG7 YOR135C IDH2 SIA1 RUP1 YOR139C SFL1
ARP8
BAG7 YOR135C IDH2 SIA1 RUP1 YOR139C SFL1
ARP8 LSC1 THI80 ELG1 PNO1 YOR146W MDM32
SPP2 SMP3 MRPL23 RPB2 YOR152C PDR5 YOR154W
ISN1 NFI1
YOR154W ISN1 NFI1 PUP1 PET123 SME1 MTR10
PNS1 YOR161C-C YOR161W-A YOR161W-B YRR1
DCI1 LAS17 RPS30B FYV12 SER1 GSP2 YOR186C-A
YOR186W TUF1 MSB1 IES4 SPR1 RIS1 YOR192C
RIS1 YOR192C YOR192C-C PEX27 TOA1 SLK19 LIP5
MCA1 BFR1 YOR199W YOR200W PET56 HIS3
YOR203W DED1
RPB10 MGM1 STE4 SAS5 YOR214C YOR215C RUD3
RFC1 YOR218C STE13 YOR220W MCT1
WTM1 YOR231C-A MKK1 MGE1 KIN4 RPL33B
YOR235W DFR1 HES1 YOR238W ABP140 YOR240W
MET7 SSP2 PUS7 ESA1 DGA1 YOR246C SRL1
YOR248W APC5 CLP1 YOR251C RBF17 NAT5 SEC63
OSW1
ESA1 DGA1 YOR246C SRL1 YOR248W APC5 CLP1
YOR251C RBF17 NAT5 SEC63 OSW1 YOR256C
CDC31 HNT3 RPT4 GCD1 RPN8 YOR262W YOR263C
DSE3 RBL2 PNT1 HRK1 YOR268C PAC1
VPH1 YOR271C YTM1 TPO4 MOD5 RIM20 CAF20
YOR277C HEM4 RFM1 FSH3 PLP2 YOR282W
YOR283W HUA2 YOR285W FMP31 YOR287C MPD1
YOR289W SNF2
FSH3 PLP2 YOR282W YOR283W HUA2 YOR285W
FMP31 YOR287C MPD1 YOR289W SNF2 YOR291W
YOR292C YOR293C-A RPS10A RRS1 UAF30
YOR296W TIM18 MBF1 YOR298W BUD7 YOR300W
RAX1 YOR302W CPA1 YOR304C-A ISW2 YOR305W
MCH5
BUD7 YOR300W RAX1 YOR302W CPA1 YOR304C-A
ISW2 YOR305W MCH5 SLY41 SNU66 YOR309C
M15_930110_937
036
NOP58
PRO2 FRT1 YOR325W MYO2 SNC2 PDR10 SCD5
YOR329W-A MIP1 YOR331C VMA4 YOR333C MRS2
YOR335W-A
SCD5 YOR329W-A MIP1 YOR331C VMA4 YOR333C
MRS2 ALA1 YOR335W-A KRE5 TEA1
15
930110
937036
15
945781
945781
15
968429
968429
UBC11 RPA43 RPA190 YOR342C YOR343C TYE7
15
970605
970605
RPA190 YOR342C YOR343C TYE7
15
103149
5
103165
7
M15_1065719_10
75593
15
106571
9
107559
3
M16_70847_7085
3
16
70847
70853
M16_84943_1044
23
16
84943
104423
M16_105260_128
717
16
105260
128717
M16_182953_207
356
16
182953
207356
M16_239627_252
119
16
239627
252119
M16_256358_280
629
16
256358
280629
16
318068
318068
16
336013
336013
16
368086
368296
M16_387239_420
441
16
387239
420441
M16_428612_429
188
16
428612
429188
PIP2 YOR364W YOR365C YOR366W SCP1 RAD17
RPS12 MRS6 GPB1 NDD1 NUD1 ALD4
FRE3 YOR381W-A FIT2 FIT3 FRE5 YOR385W PHR1
YOR387C FDH1 YOR389W YOR390W HSP33
YOR392W ERR1 YOR394C-A YOR394W
GYP5 RPL36B ICY2 YPL250W-A YPL251W YAH1
VIK1 HFI1 BBP1 CLN2 YPL257W
FAS2 SSO1 NSL1 TFP3 RVB2 YPL236C SUI3 YPL238C
YAR1 HSP82 CIN2 IQG1 SRP68 HUT1 YPL245W
RBD2 YPL247C GAL4 GYP5 RPL36B YPL250W-A
PCL8 RPL1A BOP1 YPL222C-A FMP40 GRE1 MMT2
YPL225W NEW1 ALG5 CET1 YPL229W USV1 FAS2
SSO1 NSL1 TFP3 RVB2 YPL236C SUI3 YPL238C
YAR1 HSP82 CIN2
YPL176C CUP9 CBC2 PPQ1 TCO89 CTI6 YPL182C
YPL183C YPL183W-A YPL184C YPL185W UIP4
MF(ALPHA)1 POS5 YPL189C-A GUP2 NAB3 YPL191C
PRM3 RSA1 DDC1 APL5 OXR1 YPL197C RPL7B
PEP4 KIP2 PRM4 TGS1 YPL158C PET20 CDC60 BEM4
YPL162C SVS1 MLH3 SET6 YPL166W REV3
YPL168W MEX67
UME1 MKK2 YPL141C YPL142C RPL33A YPL144W
KES1 RRP16 PXA1 PPT2 ATG5 YPL150W PRP46
RRD2 YPL152W-A RAD53 PEP4 KIP2 PRM4 TGS1
YPL158C PET20 CDC60
MRP51 DBP1 YPL119C-A VPS30 MEI5 TFB2 RNY1
SPC29 KAP120 NAN1 HHO1
YPL110C CAR1 PEX25 YPL113C YPL114W BEM3
HOS3 IDI1 MRP51
RPS6A GLR1 SSU1 NOG1 SEC62 YPL095C ERI1 PNG1
MSY1 YPL098C FMP14 ATG21 ELP4 YPL102C FMP30
CWC27 VPS28 YPL066W YPL067C YPL068C BTS1
MUK1 YPL071C UBP16 YPL073C YTA6 GCR1 GPI2
YPL077C ATP4 RPL21B YPL080C RPS9A MOT1
SEN54 BRO1 SEC16 ELP3 YDC1 YPL088W RLM1
RPS6A
LPE10 ALD6 YPL062W TIM50 CWC27 VPS28
YPL066W YPL067C YPL068C BTS1 MUK1 YPL071C
UBP16 YPL073C
M16_437335_437
335
16
437335
437335
M15_945781_945
781
M15_968429_968
429
M15_970605_970
605
M15_1031495_10
31657
M16_318068_318
068
M16_336013_336
013
M16_368086_368
296
GRX5 LPE10 ALD6 YPL062W TIM50 CWC27 VPS28
M16_437789_437
789
M16_438353_438
353
M16_438365_438
365
M16_438807_438
807
M16_438825_438
825
M16_439137_439
137
M16_439179_439
179
M16_439581_439
581
M16_441281_441
281
M16_441731_441
731
M16_442041_442
041
M16_442503_442
503
M16_445372_454
307
M16_462646_462
646
16
437789
437789
GRX5 LPE10 ALD6 YPL062W TIM50 CWC27 VPS28
16
438353
438353
PDR12 GRX5 LPE10 ALD6 YPL062W TIM50 CWC27
16
438365
438365
16
438807
438807
16
438825
438825
16
439137
439137
16
439179
439179
PDR12 GRX5 LPE10 ALD6 YPL062W TIM50
16
439581
439581
PDR12 GRX5 LPE10 ALD6 YPL062W TIM50
16
441281
441281
PDR12 GRX5 LPE10 ALD6 YPL062W
16
441731
441731
16
442041
442041
16
442503
442503
SUR1 PDR12 GRX5 LPE10 ALD6
16
445372
454307
16
462646
462646
M16_486637_497
425
16
486637
497425
M16_500342_500
354
16
500342
500354
M16_511400_523
450
16
511400
523450
M16_533282_555
416
16
533282
555416
M16_590622_604
010
16
590622
604010
M16_618575_620
596
16
618575
620596
M16_695782_700
280
16
695782
700280
M16_704388_711
614
16
704388
711614
DIG1 MNN9 ARL3 OAZ1 KTR6 LEE1 LGE1 YPL056C
SUR1 PDR12 GRX5
NOP4 YPL044C VPS16 ELC1 SGF11 CAM1 DIG1
MNN9 ARL3 OAZ1 KTR6 LEE1 LGE1 YPL056C
MET12 NCE4 YPL025C SKS1 SMA1 ERG10 SUV3
YPL030W PHO85 SVL3 YPL033C YPL034W YPL035C
PMA2 EGD1 MET31 YPL038W-A YPL039W ISM1
RAD1 MET12 NCE4 YPL025C SKS1 SMA1 ERG10
SUV3 YPL030W PHO85
RRP12 MRPS16 YPL014W HST2 SWI1 YPL017C
CTF19 VTC3 ULP1 ECM23 RAD1 MET12 NCE4
YPL025C SKS1
HAT1 SNF8 ULA1 LSP1 AEP3 NCR1 TFC8 CHL1
YPL009C RET3 TAF3 RRP12 MRPS16 YPL014W HST2
CIT3 YPR002C-A PDH1 YPR003C YPR004C
YPR011C YPR012W YPR013C YPR014C YPR015C
TIF6 YPR016W-A DSS4 RLF2 CDC54 ATP20 AGC1
YPR022C EAF3 YME1 CCL1
EAF3 YME1 CCL1 ATH1 YPR027C YOP1 APL4 CSR2
MED1 YPR071W NOT5 LTP1 TKL1 YPR074W-A OPY2
YPR076W YPR077C YPR078C MRL1 TEF1 GRS2 DIB1
MDM36 YPR084W YPR085C
YPR074W-A OPY2 YPR076W YPR077C YPR078C
MRL1 TEF1 GRS2 DIB1 MDM36 YPR084W YPR085C
SUA7 VPS69 SRP54 YPR089W YPR090W YPR091C
YPR092W ASR1 RDS3
M16_718892_718
893
16
718892
718893
16
744530
748158
16
787283
787283
16
819247
819251
M16_825431_825
431
16
825431
825431
M16_890898_897
526
16
890898
897526
16
927500
927506
16
932310
932538
M16_744530_748
158
M16_787283_787
283
M16_819247_819
251
M16_927500_927
506
M16_932310_932
538
YPR085C SUA7 VPS69 SRP54 YPR089W YPR090W
YPR091C YPR092W ASR1 RDS3 SYT1 YPR096C
YPR097W
FHL1 COG4 ISR1 YTH1 RPN7 YPR108W-A YPR109W
RPC40 DBF20 MRD1 PIS1 YPR114W YPR115W
THI22 AXL1 YPR123C CTR1 YPR125W YPR126C
YPR127W ANT1 SCD6 YPR130C NAT3 RPS23B IWS1
MEP3 VPS66 TAZ1 KAR3 YPR142C RRP15 NOC4
ASN1 YPR146C YPR147C YPR148C
KAR3 YPR142C RRP15 NOC4 ASN1 YPR146C
YPR147C YPR148C NCE102 YPR150W SUE1
YPR152C YPR153W PIN3
YPR169W-A YPR170C YPR170W-A YPR170W-B BSP1
YPR172W VPS4 YPR174C DPB2 BET2 YPR177C PRP4
HDA3 AOS1 SEC23 SMX3 DPM1 GDB1
RPC82 QCR2 AQY1 HPA2 OPT2 YPR195C YPR196W
YPR197C SGE1
AQY1 HPA2 OPT2 YPR195C YPR196W YPR197C
SGE1 ARR1 ARR2 ARR3
Table 3: Module Summary
As we mentioned in the paper, using a range of available resources, we found statistically
significant experimental support for 13 of these modules, and weaker support for an
additional 40 modules.
Module: Module id.
Size: Number of genes in module (table sorted by this column).
Annotation: Module annotation when large fraction of module genes fit a coherent
annotation.
Self: Aquamarine highlight indicates that module contains cis-regulated genes (i.e. genes
that are regulated by their own marker). The number indicated the number of such genes
in the module. Note, most of the cis-regulated genes appear in 82 modules that contain
only 1-2 genes (See table 5 in this supplement.)
Chromo: Purple highlight indicates that module is defined as a chromosomal based on its
gene set. (See Figure 3 and Methods).
Signficant: Module gene set are known targets of one of the predicted regulators in the
module regulatory program. The module gene set either has significant enrichment for
targets (as indicated by the pvalue) or over 50% of the module genes are known targets.
Supported/Related: Some support exists for a match between the modules genes and the
regulators predicted in the regulation program. Regulators are indicated in this column the
module contains a number of its known targets, but these don’t pass the significance to be
included in the previous column. Additionally, a regulator is listed if there is a match
between a process or function statistically enriched in the gene set and the known role of
that regulator.
Top, Child 1, and Child 2: Regulators appearing in the top two layers of the regulation tree
(full list of regulators for each module appears in table 5 of this supplement) Color coded
by regulator type: Blue – transcription factors; Orange – signaling protein; Purple –
chromatin modification factor; Yellow – Protien regulation (translation and degredation);
Light green – RNA processing factor; Aquamarine – G-reg of unknown mechanism
(when mechanism was known e.g. rif2 it was colored according to mechanism e.g. purple)
Note, predicted regulators capture a broad range of mechanisms, support exists for a
number of transcription factors, signaling proteins and chromatin modifying factors.
Genotype: Any genotype that exists in the modules regulatory program (including at lower
levels of the tree). When additional evidence points to one of the genes in the marker
region as being the most likely causal explanation, this gene is listed.
Module
Size
Annotation
51
219
64
217
84
130
15
122
36
114
Supported
/Related
Top
Child 1
Child 2
rRNA processing
Sap185
SAP185
SAP185
SAP185
ribosomal proteins
mitochondrial
ribosome
energy and
carbohydrate
metabolism
Amino Acid
metabolism
Ppt1
UBC9
PPT1
HHF2
Hap4
GCN20
TEA1
CAF17
Cyr1
GPG1
YAK1
CYR1
MET28
HTA1
STB4
Self
Chromo
Significant
Met28
(Gcn4 e-
Genotype
M4_1022764_1039379
56)
46
110
75
90
63
88
58
78
37
61
mitochondrial
Chromatin
remodeling
60
Amine metabolism
39
57
Bub1 targets
38
56
33
51
20
46
71
46
53
45
22
42
30
42
76
42
16
36
68
36
12
35
48
33
55
32
Mating
40
31
Nucleosome
23
30
44
28
54
26
86
26
5
24
83
24
14
23
50
23
31
20
GLN3
HTB2
BAS1
CHK1
RIM101
PSK1
ISW2
SLN1
SLN1
SIP4
FRM2
UBC9
sap185
SAP185
YVH1
PDE1
Sip4
SIP4
NRG1
MAL13
USV1
KNS1
USV1
GCN20
M12_
1056097_1056103
SIP4
TEA1
Rif2 (via
rap1)
PKH2
CYR1
M12_1056097_1056103
[Rif2]
Hap1 e-12
M12_
659357_674651
HSL1
BAS1
M12_659357_674651
[Hap1]
MET28
GCN20
YNL305C
STD1
UGA3
STD1
USV1
MDG1
USV1
MET28
GAC1
TPK1
REF2
HAC1
PNC1
SST2
ASK10
KAR4
ATG1
RPB8
ASK10
NRG1
MED1
PUF6
SIP2
TEA1
PHO81
M3_
79091_92391
M12_
659357_674651
SKM1
RAS1
M13_
27644_28694
Isw2 3.1e8
Sst2
(Ste12 e21)
2
Kar4
SIP4
PNC1
CAF17
CHK1
M12_659357_674651
AKR1
M12_
659357_674651
CAF17
MIG3
GPG1
KNS1
AMN1
STD1
CLB1
SAP4
BCY1
SPS1
spt21,
SPT21
STB4
IXR1
gpa1
MFA2
M2_
562409_570229
GPA1
NRG1
MSB2
GCN20
SKM1
CYR1
Hap1 e-7
cytoskeleton
19
1
16
43
16
99
16
Mitochondrial
MFA2
1
M14M4_85846_106892
M13_27644_28694
M3_79091_92391
[Leu2]
Lue2 e-10
(Leu3)
3
87
ELP3
PSK1
chk1
6
ELP3
GCR1
Mitochondria and
transport
Cell cycle and bud
neck
Mating alpha
targets
Cell wall and bud
neck
PNC1
SEF1
Gcr1, Psk1
Amine metabolism
Leu3 targets
LSG1
CUP2
met28 e-4
32
PNC1
CUP2
rRNA processing
69
KIN82
HAC1
Bas1 3.4e5
3
Telomere
Lipid and
Ergostorol
metabolism
Alcohol
metabolism
Lipid
metabolism
PDE1
CHK1
Unknown
Transport and
Eneregy
11
ROM1
amn1
cyr1
M12_659357_674651
[Hap1]
M2_562409_570229
[Amn1]
9
15
29
15
57
15
65
15
18
14
matalpha1
(ste12 e-7)
Mating
21
14
94
13
Sugar metabolism
100
13
109
12
4
10
79
10
17
9
35
9
GPA1
M14_
206186_209852
IME1
MTH1
SWI1
MATALPHA1
1
DNA Damage
response
BMH1
Rad53,
Dun1
1
PIP2
YNL305C
CDC27
UBC9
MTH1
RAD53
M14_
486861_486861
CDC5
DUN1
LAP3
SNF8
M14_486861_486861
CLN3
M13_46070_69122
ZAP1
RPB10
M10_
336317_353027
CDC5
IME1
SIP4
MTF1
UGA3
XBP1
M13_
46070_69122
Zinc response
zap1
KAR4
YPR013C
SAP185
Signaling
MED1
78
9
49
8
85
8
90
8
PTC5
RSC30
3
7
HTA1
DUN1
52
7
5
UGA3
73
7
4
SLT2
M7_
375499_375499
81
7
UPC2
M12_
1042072_1054302
M11_
643655_643655
PTP1
ZAP1
FZF1
ura3
1
cell wall
Oxireductase
activity
3
Slt2
1
M5_109310_117705
[Ura3]
SKM1
M13_905780_922268
AMN1
6
6
24
6
27
6
SIP4
PKH2
62
6
IRA1
70
6
97
6
PTC4
M15_
1152_43217
M8_
80014_95469
108
6
CUP2
M10_
646911_646911
M15_
1152_43217
M1_
51324_52943
M4_
527445_527517
M9_
214482_254745
M4_
85846_106892
M12_
450041_508029
MET28
1
mating
vitamin
biosynthesis
3
111
6
2
7
5
26
5
Lipid metabolism
1
67
5
ion transport
4
56
4
4
72
4
3
89
4
2
4
GPA1
SAP185
M1_
1_37068
M10_
22213_34098
M5_553222_568734
M1_1_37068
M10_22213_34098
M7_375499_375499
7
Zap1
GCR1
MIH1
93
Sir1
M9_415311_420076
XBP1
BCY1
M5_
109310_117705
M13_
905780_922268
M5_
553222_568734
pyrimidine
synthesis
M14_206186_209852
SAP4
PSK1
PUF6
M12_1042072_1054302
M11_643655_643655
[Sir1]
UBC9
STB4
UBC9
M5_99004_99004
M15_1152_43217
M8_80014_95469
[Gpa1]
M10_646911_646911
M15_1152_43217
PPT1
MSN4
M1_51324_52943
M4_527445_527517
KAR4
PTI1
M9_214482_254745
M4_85846_106892
M12_450041_508029
101
4
10
3
2
M5_
109310_117705
M11_
643655_643655
M5_109310_117705
GPA1
M11_643655_643655
Table 4: Module Annotation
We evaluated the biological relevance of each the 165 modules in the context of other
genomic datasets. We used the hyper-geometric p-value to test for functional enrichment of
1601 GO categories taken from SGD. To associate transcription factors (and sometimes
their known upstream signaling molecule) to targets we used ChIP binding data as well as a
map of predicted binding sites in promoter regions (see Additional data sources in
Supplementary methods). All reported pvalues are FDR corrected for multiple testing.
Annotation
sex determination
transcription factor binding
regulation of transcription,
mating-type specific
Lieb01_SIR2
Lieb01_SIR3
Lieb01_SIR4
cell adhesion
one-carbon
compound
metabolism
oxidoreductase
activity,
acting on the CH-NH2 group
of donors
Harbison04_BAS1_YPD
vacuole
fusion,
nonautophagic
acid phosphatase activity
PHO4
Harbison04_PHO4_Piorganic acid metabolism
amine metabolism
amine biosynthesis
aromatic
compound
metabolism
aromatic amino acid family
metabolism
cell wall organization and
biogenesis
Harbison04_HAP1_YPD
carbohydrate metabolism
response to stimulus
energy reserve metabolism
response to stress
fermentation
alcohol
dehydrogenase
activity
glutamine family amino acid
metabolism
Hits
4
4
#Genes in
Module
16
16
%
25
25
#Genes
with
annotation
7
16
6.61E-09
4.08E-07
3.69E-07
2.78E-08
8.00E-07
4
7
6
7
3
16
12
12
12
7
25
58.34
50
58.34
42.86
6
86
50
59
10
4
6.40E-09
4
10
40
9
4
4
1.91E-06
1.21E-06
3
4
10
10
30
40
9
28
9
9
9
9
11
11
11
4.82E-06
1.66E-09
4.40E-07
1.01E-12
1.84E-09
6.05E-08
6.93E-09
3
4
4
6
19
15
13
15
15
15
15
60
60
60
20
26.67
26.67
40
31.67
25
21.67
8
5
15
10
202
150
91
11
1.57E-09
10
60
16.67
40
11
1.62E-07
6
60
10
15
13
14
15
15
15
15
24
8.25E-06
1.16E-07
1.22E-08
2.01E-06
2.06E-08
1.67E-07
8.38E-07
6
7
20
23
8
22
3
30
23
122
122
122
122
6
20
30.44
16.4
18.86
6.56
18.04
50
54
57
119
205
15
165
12
24
3.83E-08
3
6
50
5
28
1.09E-06
4
8
50
37
Module
ID
1
1
P-value
1.54E-08
7.78E-07
1
1
1
1
3
response to extracellular
stimulus
hydrolase activity, acting on
carbon-nitrogen (but not
peptide) bonds
carbon-nitrogen (but not
peptide) bonds, in linear
amides
aspartate family amino acid
metabolism
catabolism
amine catabolism
asparagine metabolism
response to starvation
catabolism
asparaginase activity
periplasmic space
DNA recombination
helicase activity
response to DNA damage
stimulus
telomere maintenance
mitotic recombination
DNA helicase activity
telomerase-independent
telomere maintenance
PDR1
Harbison04_PDR1_YPD
Harbison04_YAP5_YPD
Harbison04_GAT3_YPD
Lieb01_RAP1
Lieb01_SIR2
Lieb01_SIR4
Lieb01_RAP1
Lieb01_SIR2
Lieb01_SIR4
organic acid metabolism
amine metabolism
amine biosynthesis
metabolism
biosynthesis
arginine biosynthesis
arginine metabolism
transaminase activity
metabolism
28
8.37E-09
4
8
50
12
28
5.96E-07
4
8
50
32
28
4.01E-08
4
8
50
17
28
1.35E-06
4
8
50
39
28
28
28
28
2.14E-09
8.13E-08
2.14E-09
3.56E-09
4
4
4
4
8
8
8
8
50
50
50
50
9
20
9
10
28
28
28
30
30
3.56E-09
8.52E-11
5.95E-10
5.57E-08
1.20E-18
4
4
4
7
15
8
8
8
42
42
50
50
50
16.67
35.72
10
5
7
29
45
30
30
30
30
2.52E-06
7.17E-11
5.16E-12
1.41E-11
7
7
7
7
42
42
42
42
16.67
16.67
16.67
16.67
49
13
10
11
30
30
30
30
30
30
30
30
31
31
31
36
36
36
1.56E-12
9.27E-07
1.60E-06
1.45E-10
9.73E-10
1.32E-15
5.36E-10
8.45E-10
1.38E-10
5.12E-25
1.12E-07
6.59E-24
2.42E-27
8.73E-32
7
4
5
7
6
29
14
12
17
19
8
43
41
37
42
42
20
20
20
37
37
37
20
20
20
114
114
114
16.67
9.53
25
35
30
78.38
37.84
32.44
85
95
40
37.72
35.97
32.46
9
7
33
27
19
314
86
59
314
86
59
202
150
91
36
2.43E-09
12
114
10.53
37
36
36
36
36
4.19E-10
2.59E-15
6.75E-13
5.89E-07
11
10
10
7
114
114
114
114
9.65
8.78
8.78
6.15
26
10
13
16
36
2.08E-11
14
114
12.29
39
biosynthesis
sulfur metabolism
sulfur amino acid metabolism
methionine metabolism
nonprotein
amino
acid
metabolism
ornithine metabolism
sulfur utilization
GCN4
GLN3
Harbison04_GCN4_RAPA
Harbison04_GCN4_SM
Harbison04_GCN4_YPD
Harbison04_GLN3_RAPA
carrier activity
aerobic respiration
energy pathways
oxidoreductase activity
cofactor metabolism
coenzyme metabolism
cation transporter activity
ion transporter activity
cation transport
ion transport
coenzyme biosynthesis
phosphorylation
phosphate metabolism
respiratory chain complex III
primary active transporter
activity
hydrogen ion transporter
activity
monovalent inorganic cation
transport
respiratory chain complex IV
purine nucleotide metabolism
nucleotide metabolism
nucleotide biosynthesis
ribonucleotide metabolism
succinate
dehydrogenase
(ubiquinone) activity
tricarboxylic
acid
cycle
intermediate metabolism
main
pathways
of
carbohydrate metabolism
tricarboxylic acid cycle
group transfer coenzyme
metabolism
nucleoside
triphosphate
metabolism
36
36
36
36
1.48E-09
9.16E-09
1.48E-06
1.24E-07
9
12
8
8
114
114
114
114
7.9
10.53
7.02
7.02
17
41
25
19
36
36
36
36
36
36
36
36
36
37
37
37
37
37
37
37
37
37
37
37
37
37
37
1.51E-07
3.31E-07
2.91E-06
9.91E-56
1.43E-06
5.97E-29
1.71E-23
5.67E-19
1.11E-05
9.69E-18
1.53E-15
1.32E-22
1.20E-13
5.21E-13
1.59E-14
3.89E-30
5.33E-27
8.71E-14
6.71E-13
2.45E-17
1.59E-14
1.98E-13
1.09E-13
6
5
5
55
10
34
32
21
9
18
15
27
23
16
15
26
26
14
15
14
15
15
8
114
114
114
114
114
113
113
113
113
61
61
61
61
61
61
61
61
61
61
61
61
61
61
5.27
4.39
4.39
48.25
8.78
30.09
28.32
18.59
7.97
29.51
24.6
44.27
37.71
26.23
24.6
42.63
42.63
22.96
24.6
22.96
24.6
24.6
13.12
9
6
8
108
42
82
97
46
40
62
47
130
190
80
54
65
82
49
68
30
54
63
9
37
3.99E-19
15
61
24.6
30
37
2.35E-41
26
61
42.63
33
37
37
37
37
37
37
6.04E-20
1.09E-13
3.65E-16
3.12E-12
5.09E-15
1.72E-18
14
8
14
14
14
14
61
61
61
61
61
61
22.96
13.12
22.96
22.96
22.96
22.96
22
9
35
62
41
26
37
6.26E-07
4
61
6.56
5
37
8.53E-06
5
61
8.2
16
37
37
1.07E-07
3.85E-13
9
9
61
61
14.76
14.76
45
14
37
1.72E-18
14
61
22.96
26
37
7.53E-21
14
61
22.96
20
proton-transporting
ATP
synthase complex, coupling
factor F(o)
hydrogen-transporting ATP
synthase activity, rotational
mechanism
ATP metabolism
HAP3
HAP4
HAP2
Harbison04_HAP4_YPD
nucleic acid binding
DNA metabolism
nuclear organization and
biogenesis
DNA packaging
DNA binding
chromatin
assembly
or
disassembly
nucleosome
MBP1
cell wall
glycosyl bonds
glucosidase activity
bud neck
beta-glucosidase activity
cytokinesis, completion of
separation
ACE2
SWI5
amine metabolism
RNA ligase activity
autophagy
RNA metabolism
RNA processing
ribosome assembly
RNA binding
rRNA processing
ribosome biogenesis
ribosome-nucleus export
processing of 20S pre-rRNA
nucleolus
RNA modification
RNA helicase activity
helicase activity
ribonucleoprotein complex
ATP-dependent
helicase
activity
37
2.30E-09
5
61
8.2
5
37
37
37
37
37
37
40
40
5.57E-20
2.47E-23
6.32E-08
8.83E-31
4.70E-07
4.66E-17
3.98E-06
8.44E-08
11
14
6
21
7
14
11
10
61
61
61
61
61
61
31
31
18.04
22.96
9.84
34.43
11.48
22.96
35.49
32.26
11
16
13
31
27
30
222
118
40
40
40
5.36E-10
3.84E-10
1.36E-10
10
9
11
31
31
31
32.26
29.04
35.49
71
49
84
40
40
40
43
4.10E-14
2.39E-18
1.31E-06
1.15E-06
8
9
7
6
31
31
31
16
25.81
29.04
22.59
37.5
13
10
61
77
43
43
43
43
2.66E-07
7.78E-07
1.12E-05
2.13E-06
5
4
4
3
16
16
16
16
31.25
25
25
18.75
31
16
30
6
43
43
43
44
44
46
51
51
51
51
51
51
51
51
51
51
51
51
51
51
2.13E-06
5.81E-13
5.03E-07
3.13E-06
1.79E-06
2.22E-06
2.57E-65
4.34E-13
1.20E-64
8.78E-06
5.69E-18
8.83E-77
1.82E-15
5.38E-08
2.24E-30
3.25E-74
3.20E-09
1.99E-12
1.82E-08
1.45E-14
3
7
5
9
5
6
94
47
83
5
37
82
15
7
33
78
17
15
16
29
16
16
16
28
28
110
219
219
219
219
219
219
219
219
219
219
219
219
219
219
18.75
43.75
31.25
32.15
17.86
5.46
42.93
21.47
37.9
2.29
16.9
37.45
6.85
3.2
15.07
35.62
7.77
6.85
7.31
13.25
6
18
35
150
25
13
189
222
142
6
106
111
18
8
44
103
46
24
45
81
51
7.25E-10
12
219
5.48
20
RNA-dependent
ATPase
activity
35S
primary
transcript
processing
ribosomal
large
subunit
assembly and maintenance
ribosomal subunit assembly
ribosomal
large
subunit
biogenesis
processing of 27S pre-rRNA
small
nucleolar
ribonucleoprotein complex
snoRNA binding
rRNA modification
rRNA binding
RNA polymerase complex
MCM1
STE12
Harbison04_STE12_BUT14
protein biosynthesis
translation factor activity,
translation regulator activity
RNA binding
large ribosomal subunit
structural
constituent
of
ribosome
small ribosomal subunit
regulation of biosynthesis
ribosomal
large
subunit
ribosomal subunit assembly
translation initiation factor
activity
cytosolic small ribosomal
subunit (sensu Eukaryota)
translational elongation
regulation of translation
cytosolic large ribosomal
subunit (sensu Eukaryota)
ribosomal small subunit
regulation of translational
fidelity
RAP1
FHL1
SFP1
Harbison04_FHL1_YPD
Harbison04_RAP1_YPD
Harbison04_FHL1_RAPA
51
4.30E-11
12
219
5.48
17
51
1.74E-29
30
219
13.7
37
51
51
2.95E-10
6.99E-08
15
15
219
219
6.85
6.85
31
43
51
51
1.62E-12
1.05E-07
11
6
219
219
5.03
2.74
12
6
51
51
51
51
51
57
57
57
64
64
3.11E-21
2.29E-23
1.00E-06
2.62E-06
9.00E-07
2.56E-07
2.20E-07
3.59E-06
1.51E-08
3.70E-105
22
22
8
6
9
5
7
5
39
130
219
219
219
219
219
15
15
14
217
217
10.05
10.05
3.66
2.74
4.11
33.34
46.67
35.72
17.98
59.91
28
25
14
8
18
33
107
57
222
234
64
64
64
64
8.93E-06
4.58E-06
4.22E-09
1.26E-62
11
12
26
75
217
217
217
217
5.07
5.53
11.99
34.57
34
38
106
117
64
64
64
5.23E-116
8.84E-47
6.06E-07
128
55
10
217
217
217
58.99
25.35
4.61
197
82
22
64
64
3.18E-06
4.19E-14
11
21
217
217
5.07
9.68
31
43
64
1.06E-05
8
217
3.69
18
64
64
64
5.71E-66
3.54E-06
4.34E-09
55
8
10
217
217
217
25.35
3.69
4.61
56
16
15
64
1.51E-86
75
217
34.57
80
64
1.15E-10
10
217
4.61
12
64
64
64
64
64
64
64
6.69E-09
1.04E-47
6.26E-86
4.32E-28
6.82E-50
9.44E-25
1.09E-48
7
55
84
26
57
33
58
217
217
217
217
184
184
184
3.23
25.35
38.71
11.99
30.98
17.94
31.53
7
80
103
29
90
63
97
Harbison04_FHL1_SM
Harbison04_SFP1_SM
Lieb01_RAP1
ATPase activity, coupled to
transmembrane movement of
substances
metal ion transport
P-P-bond-hydrolysis-driven
transporter activity
primary active transporter
activity
monovalent inorganic cation
transport
ATPase activity, coupled to
transmembrane movement of
ions,
phosphorylative
mechanism
membrane lipid metabolism
glycerophospholipid
metabolism
phospholipid metabolism
phospholipid biosynthesis
organelle lumen
endoplasmic reticulum lumen
development
reproduction
membrane fusion
site of polarized growth
shmoo tip
G-protein coupled receptor
protein signaling pathway
cell surface receptor linked
signal transduction
DIG1
STE12
TEC1
Harbison04_STE12_BUT90
Harbison04_DIG1_Alpha
oxidoreductase
activity,
acting on paired donors, with
incorporation or reduction of
molecular oxygen
lipid metabolism
lipid biosynthesis
alcohol metabolism
endoplasmic reticulum
endoplasmic
reticulum
membrane
sterol metabolism
steroid biosynthesis
ergosterol metabolism
64
64
64
4.55E-43
9.68E-15
1.45E-46
56
16
106
184
184
159
30.44
8.7
66.67
105
24
314
67
67
8.51E-06
4.93E-06
3
3
5
5
60
60
31
26
67
5.46E-07
3
5
60
13
67
7.69E-06
3
5
60
30
67
2.93E-06
3
5
60
22
67
68
1.61E-07
7.00E-07
3
6
5
36
60
16.67
9
30
68
68
68
68
68
69
69
69
69
69
6.65E-06
5.30E-06
9.53E-06
2.12E-07
7.12E-08
4.73E-09
4.12E-07
1.11E-05
1.26E-08
5.35E-13
4
5
4
4
4
10
6
4
8
8
36
36
36
36
36
32
32
32
32
32
11.12
13.89
11.12
11.12
11.12
31.25
18.75
12.5
25
25
12
24
13
6
5
85
31
15
48
16
69
4.10E-06
4
32
12.5
12
69
69
69
69
69
69
1.11E-05
2.04E-19
5.74E-21
3.32E-16
5.16E-08
5.40E-07
4
16
19
11
7
6
32
32
32
32
32
32
12.5
50
59.38
34.38
21.88
18.75
15
69
107
28
36
31
76
76
76
76
76
9.27E-07
4.79E-22
4.72E-25
6.75E-20
5.94E-12
4
21
19
20
14
42
42
42
42
42
9.53
50
45.24
47.62
33.34
7
96
50
102
96
76
76
76
76
7.20E-08
1.20E-34
1.21E-32
1.79E-32
7
20
19
18
42
42
42
42
16.67
47.62
45.24
42.86
30
27
26
22
HAP1
Harbison04_HAP1_YPD
intracellular transport
protein transport
protein-mitochondrial
targeting
protein transporter activity
mitochondrial
inner
membrane protein import
mitochondrial matrix protein
import
mitochondrial intermembrane
space
inner membrane
aerobic respiration
mitochondrion
protein complex assembly
protein biosynthesis
tRNA aminoacylation
RNA ligase activity
organellar large ribosomal
subunit
large ribosomal subunit
structural
constituent
of
ribosome
small ribosomal subunit
organellar small ribosomal
subunit
Lieb01_SIR2
Lieb01_SIR3
Lieb01_SIR4
amine biosynthesis
branched chain family amino
acid metabolism
LEU3
Harbison04_LEU3_YPD
Harbison04_LEU3_SM
oxidoreductase
activity,
acting on CH-OH group of
donors
RDS1
alcohol metabolism
carbohydrate catabolism
carbohydrate biosynthesis
hexose metabolism
gluconeogenesis
glucose metabolism
glycolysis
hexose catabolism
Harbison04_GCR2_YPD
thiamin metabolism
76
76
83
83
5.12E-16
2.37E-12
1.04E-08
9.17E-08
13
12
9
7
42
40
24
24
30.96
30
37.5
29.17
40
57
93
55
83
83
6.23E-12
3.59E-09
7
6
24
24
29.17
25
16
20
83
3.84E-06
3
24
12.5
5
83
1.78E-07
4
24
16.67
8
83
84
84
84
84
84
84
84
9.29E-06
1.17E-05
2.33E-08
2.00E-10
4.69E-08
2.66E-39
2.38E-06
3.06E-07
4
11
13
42
10
63
7
9
24
130
130
130
130
130
130
130
16.67
8.47
10
32.31
7.7
48.47
5.39
6.93
19
56
47
373
27
234
17
25
84
84
1.64E-43
2.85E-20
33
33
130
130
25.39
25.39
37
117
84
84
1.40E-34
3.77E-13
55
22
130
130
42.31
16.93
197
82
84
85
85
85
86
7.38E-28
4.86E-09
1.22E-08
3.44E-08
5.58E-06
22
7
6
6
7
130
8
8
8
26
16.93
87.5
75
75
26.93
26
86
50
59
91
86
86
86
86
3.45E-06
3.16E-15
1.32E-07
4.71E-10
4
8
5
7
26
26
26
26
15.39
30.77
19.24
26.93
14
12
16
24
93
93
94
94
94
94
94
94
94
94
94
111
5.17E-06
1.78E-09
1.42E-06
2.10E-06
7.54E-06
1.06E-06
4.02E-07
1.76E-07
8.47E-08
3.08E-07
4.84E-07
1.73E-06
4
4
6
4
4
5
4
5
4
4
4
3
7
7
13
13
13
13
13
13
13
13
13
6
57.15
57.15
46.16
30.77
30.77
38.47
30.77
38.47
30.77
30.77
30.77
50
64
10
102
25
34
51
17
36
12
16
17
15
Table 5: List of modules
For each of 165 modules, we list the expression regulators, chromosomal markers and the
module genes. These modules can be interactively viewed using our visulazation software
Genomica (can be downloaded from http://genomica.weizmann.ac.il/index.html) and the
file
containing
the
modules
information
(can
be
downloaded
from
http://ai.stanford.edu/~koller/seqvar.gxp). The visualization gives access to the modules
gene expression and annotations as well as interactive viewing of the information in this
table. For the expression regulators and module genes, it provides ORF name, gene name
and SGD desciprtion. For the genotype regulators, we listed the genes that are located
within 10kb upstream/downstream of the genomic region the markers corresponding to the
genetic regulator cover. For each of these genes, we provided the number of coding SNPs
and upstream SNPs inside the parenthesis.
(1) MODULE 1
Expression regulators
YNL145W
MFA2
YHR005C
GPA1
Module genes
YCL065W
YKL177W
None
None
YCL067C
HMLALPHA2
YCR040W
MATALPHA1
YCL066W
HMLALPHA1
YJR004C
SAG1
YGL090W
LIF1
YLR041W
YCR041W
YPL187W
None
None
MF(ALPHA)1
YCR039C
MATALPHA2
lipopeptide mating pheromone; mating a-factor pheromone
precursor
Alpha subunit of G protein coupled to mating factor receptors,
involved in the mating pheromone signal transduction pathway;
component of pheromone response pathway common to both a
and alpha cells
Silenced copy of ALPHA2, encoding a homeobox-domain
containing protein that associates with Mcm1p in haploid cells
to repress a-specific gene expression and interacts with A1p in
diploid cells to repress haploid-specific gene expression
Transcriptional co-activator involved in regulation of matingtype-specific gene expression; targets the transcription factor
Mcm1p to the promoters of alpha-specific genes; one of two
genes encoded by the alpha mating type cassette
Silenced copy of ALPHA1, encoding a transcriptional
coactivator involved in the regulation of mating-type alphaspecific gene expression
Alpha-agglutinin of alpha-cells, binds to Aga1p during
agglutination, N-terminal half is homologous to the
immunoglobulin superfamily and contains binding site for aagglutinin, C-terminal half is highly glycosylated and contains
GPI anchor
Protein involved in DNA double-strand break repair; physically
interacts with DNA ligase 4 (Lig4p); homologous to mammalian
XRCC4 protein
mating factor alpha
Homeobox-domain containing protein which, in haploid cells,
acts with Mcm1p to repress a-specific genes; in diploid cells
YOR090C
PTC5
YCR096C
HMRA2
YGL089C
YLR040C
MF(ALPHA)2
None
YKL178C
STE3
Alpha2p acts together with A1p to repress transcription of
haploid-specific genes
Silenced copy of A2, encoding a protein of with similarity to
Alpha2p that is required along with A1p for inhibiting
expression of the HO endonuclease in a/alpha HO/HO diploid
cells with an active mating-type interconversion system
alpha mating factor
Cell surface a factor receptor, transcribed in alpha cells and
required for mating by alpha cells, couples to a MAP kinase
cascade to mediate pheromone response; ligand bound receptors
undergo endocytosis and recyling to the plasma membrane
(2) MODULE 2
Genotype regulators
MUP3(0,5) YHL037C CBP2(45,5) YHL039W ARN1(3,0)
YHL041W YHL042W ECM34(2,6) YHL044W YHL045W
YHL046C YHL046W-A ARN2(308,525) YHL048C-A
COS8(79,2) YHL049C YHL050C YHL050W-A
M8_5776_19171
Module genes
YHL047C
ARN2
YHL044W
(3) MODULE 3
None
YDR225W
HTA1
YDL101C
DUN1
Transporter, member of the ARN family of transporters that
specifically recognize siderophore-iron chelates; responsible for
uptake of iron bound to the siderophore triacetylfusarinine C
One of two nearly identical (see also HTA2) histone H2A
subtypes; core histone required for chromatin assembly and
chromosome function; DNA damage-dependent phosphorylation
by Mec1p facilitates DNA repair; acetylated by Nat4p
Cell-cycle checkpoint serine-threonine kinase required for DNA
damage-induced transcription of certain target genes,
phosphorylation of Rad55p and Sml1p, and transient G2/M
arrest after DNA damage; also regulates postreplicative DNA
repair
Genotype regulators
ACS1(2,7) PEX22(3,3) YAL056C-A GPB2(10,6) CNE1(9,5)
YAL058C-A YAL059C-A ECM1(4,2) BDH1(6,5) YAL061W
GDH3(0,50) FLO9(880,506) YAL063C-A YAL064C-A
YAL064W YAL064W-B YAL065C YAL066W
SEO1(370,503) YAL067W-A YAL068C YAL068W-A
YAL069W
M1_1_37068
Module genes
YAR062W
YAL065C
YAR050W
None
None
FLO1
Lectin-like protein involved in flocculation, cell wall protein
that binds to mannose chains on the surface of other cells,
confers floc-forming ability that is chymotrypsin sensitive and
heat resistant; similar to Flo5p
YHR213W
YAL064W-B
None
None
YAL063C
FLO9
YHR211W
FLO5
Lectin-like protein with similarity to Flo1p, thought to be
expressed and involved in flocculation
Lectin-like protein involved in flocculation, cell wall protein
that binds to mannose chains on the surface of other cells,
confers floc-forming ability that is chymotrypsin resistant but
heat labile; similar to Flo1p
(4) MODULE 4
YOR210W
RPB10
YAL040C
CLN3
YPL075W
GCR1
YKL032C
IXR1
RNA polymerase subunit, found in RNA polymerase complexes
I, II, and III
role in cell cycle START; involved in G(sub)1 size control;
G(sub)1 cyclin
Transcriptional activator of genes involved in glycolysis,
functions and interacts with Gcr2p
Protein that binds DNA containing intrastrand cross-links
formed by cisplatin, contains two HMG (high mobility group
box) domains, which confer the ability to bend cisplatinmodified DNA; mediates aerobic transcriptional repression of
COX5b
Genotype regulators
VPS9(7,4) TAF13(3,0) ARG81(14,0) YML099W-A TSL1(3,1)
YML100W-A CUE4(0,0) YML101C-A YML102C-A
CAC2(2,0) NUP188(7,0) MDM1(416,120) SEC65(0,4)
URA5(0,4) YML107C YML108W ZDS2(8,7) COQ5(2,7)
BUL2(2,11) CTK3(2,0) DAT1(5,2) TAF8(2,2) VAN1(1,2)
ATR1(0,56) YML116W-A YML117W-A
M13_46070_69122
Module genes
YHR157W
REC104
YLR058C
SHM2
YDR019C
GCV1
YCL064C
CHA1
YGL255W
ZRT1
YJL056C
ZAP1
YHR111W
UBA4
Protein involved in early stages of meiotic recombination;
required for meiotic crossing over; forms a complex with
Rec102p and Spo11p necessary during the initiation of
recombination
serine hydroxymethyltransferase
T subunit of the mitochondrial glycine decarboxylase complex,
required for the catabolism of glycine to 5,10-methylene-THF;
expression is regulated by levels of levels of 5,10-methyleneTHF in the cytoplasm
catabolism of hydroxy amino acids; catabolic serine (threonine)
dehydratase
High-affinity zinc transporter of the plasma membrane,
responsible for the majority of zinc uptake; transcription is
induced under low-zinc conditions by the Zap1p transcription
factor
Zinc-regulated transcription factor, binds to zinc-responsive
promoter elements to induce transcription of certain genes in the
presence of zinc; regulates its own transcription; contains seven
zinc-finger domains
Protein that activates Urm1p before its conjugation to proteins
(urmylation); one target is the thioredoxin peroxidase Ahp1p,
YIL051C
MMF1
YAL044C
GCV3
YMR189W
GCV2
suggesting a role of urmylation in the oxidative stress response
Maintenance of Mitochondrial Function; Maintenance of
Mitochondrial DNA 1
H subunit of the mitochondrial glycine decarboxylase complex,
P subunit of the mitochondrial glycine decarboxylase complex,
(5) MODULE 5
YJR122W
CAF17
YBR274W
CHK1
YNL031C
HHT2
YDR264C
AKR1
Mitochondrial protein that interacts with Ccr4p in the twohybrid system; 3'-untranslated region contains a putative mRNA
localization element common to genes encoding mitochondrial
proteins
checkpoint kinase 1; homolog of the S. pombe and mammalian
Chk1 checkpoint kinases; Protein kinase Chk1
One of two identical histone H3 proteins (see also HHT1); core
histone required for chromatin assembly, involved in
heterochromatin-mediated telomeric and HM silencing;
regulated by acetylation, methylation, and mitotic
phosphorylation
Negative regulator of pheromone response pathway; required for
endocytosis of pheromone receptors; involved in cell shape
control; Ankyrin repeat-containing protein
Genotype regulators
YLR257W GSY2(1,6) HSP60(0,6) LCB5(10,6) VPS63(3,0)
YPT6(0,13) RBF7 RED1(13,14) YLR264C-A RPS28B(0,5)
NEJ1(7,0) PDR8(8,6) BOP2(4,6) SEC22(0,3) YLR269C
DCS1(0,4) YLR271W
M12_659357_674651
Module genes
YGR209C
TRX2
YGL179C
TOS3
YOL101C
IZH4
YGR037C
ACB1
YDR213W
UPC2
YDR518W
EUG1
YOR092W
YLR255C
ECM3
None
thioredoxin
Putative protein kinase, related to and redundant with Elm1p and
Pak1p in activating the SNF1 complex
Membrane protein involved in zinc metabolism, member of the
four-protein IZH family, expression induced by fatty acids and
altered zinc levels; deletion reduces sensitivity to excess zinc;
possible role in sterol metabolism
Acyl-CoA-binding protein, transports newly synthesized acylCoA esters from fatty acid synthetase (Fas1p-Fas2p) to acylCoA-consuming processes
involved in sterol uptake; zinc finger transcription factor of the
Zn(2)-Cys(6) binuclear cluster domain type
Protein disulfide isomerase of the endoplasmic reticulum lumen,
function overlaps with that of Pdi1p; may interact with nascent
polypeptides in the ER
Non-essential protein of unknown function
YOR377W
ATF1
YHR179W
OYE2
YER011W
TIR1
YOR229W
WTM2
YOR321W
PMT3
YBR067C
TIP1
YLR244C
MAP1
YOR175C
None
YKL008C
LAC1
YIL121W
QDR2
YLR265C
NEJ1
YDR274C
YDR297W
None
SUR2
YLR380W
CSR1
YDR044W
HEM13
YLR256W
HAP1
Alcohol acetyltransferase with potential roles in lipid and sterol
metabolism; responsible for the major part of volatile acetate
ester production during fermentation
Widely conserved NADPH oxidoreductase containing flavin
mononucleotide (FMN), homologous to Oye3p with slight
differences in ligand binding and catalytic properties; may be
involved in sterol metabolism
Cell wall mannoprotein of the Srp1p/Tip1p family of serinealanine-rich proteins; expression is downregulated at acidic pH
and induced by cold shock
WD repeat containing transcriptional modulator 2;
Transcriptional modulator
Transfers mannose residues from dolichyl phosphate-Dmannose to specific serine/threonine residues of proteins in the
secretory pathway; dolichyl phosphate-D-mannose:protein O-Dmannosyltransferase
cold- and heat-shock induced protein of the Srp1p/Tip1p family
of serine-alanine-rich proteins; cell wall mannoprotein
Methionine aminopeptidase, catalyzes the cotranslational
removal of N-terminal methionine from nascent polypeptides;
function is partially redundant with that of Map2p
Ceramide synthase component, involved in synthesis of
ceramide from C26(acyl)-coenzyme A and dihydrosphingosine
or phytosphingosine, functionally equivalent to Lag1p
Multidrug transporter responsible for resistance to quinidine and
barban; member of a family of drug:proton antiporters; plasma
membrane transporter
Nonhomologous End-Joining regulator 1; Repressed by MAT
heterozygosity; Interacts with Lif1p in a yeast two-hybrid assay;
Nonhomologous End-Joining regulator 1
Sphingosine hydroxylase; has a role in sphingolipid metabolism
Phosphatidylinositol transfer protein with a potential role in lipid
turnover; interacts specifically with thioredoxin peroxidase
(Tsa2p) and may have a role in oxidative stress resistance
Coproporphyrinogen III oxidase, an oxygen requiring enzyme
that catalyzes the sixth step in the heme biosynthetic pathway;
localizes to the mitochondrial inner membrane; transcription is
repressed by oxygen and heme (via Rox1p and Hap1p)
Heme-responsive zinc finger transcription factor of the Zn(2)Cys(6) binuclear cluster domain type; redox sensing regulator of
gene expression (activates CYC1, CYC7, CYP3, CYB2, CTT1,
COR2, ROX1, ERG9, ERG11, SOD2 and YHB1; represses
HEM13)
(6) MODULE 6
Genotype regulators
M11_643655_643655
Module genes
UBP11(1,2) YKR099C-A BAS1(2,2) SKG1(5,0) SIR1(4,0)
FLO10(878,496)
YKR103W
NFT1
YKR105C
None
YKR080W
MTD1
YKR104W
None
YKR087C
OMA1
YKR102W
FLO10
ORFs YKR103W and YKR104W are merged in different strain
backgrounds.
NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase,
plays a catalytic role in oxidation of cytoplasmic one-carbon
units; expression is regulated by Bas1p and Bas2p, repressed by
adenine, and may be induced by inositol and choline
Metalloendopeptidase of the mitochondrial inner membrane,
involved in turnover of membrane-embedded proteins; member
of a family of predicted membrane-bound metallopeptidases in
prokaryotes and higher eukaryotes
Lectin-like protein with similarity to Flo1p, thought to be
involved in flocculation
(7) MODULE 7
Genotype regulators
CTR9(13,2) PSF3(1,1) PEX11(0,1) SPT20(4,15) DCP1(0,4)
YOL150C GRE2(6,81) FRE7(38,11) YOL153C ZPS1(3,8)
YOL155C YOL155W-A HXT11(6,53) YOL157C ENB1(5,8)
YOL159C YOL159C-A YOL160W YOL161C YOL162W
YOL163W YOL164W YOL164W-A AAD15(7,561) YOL166C
YOL166W-A
M15_1152_43217
Module genes
YOL164W
None
YOL152W
FRE7
YOL162W
None
YDL161W
ENT1
YOL163W
(8) MODULE 9
None
YER177W
BMH1
YHR005C
GPA1
YPL127C
HHO1
YDR461W
Genotype regulators
M14_206186_209852
MFA1
Putative ferric reductase with similarity to Fre2p; expression
induced by low copper levels but not by low iron levels
Epsin-like protein involved in endocytosis and actin patch
assembly and functionally redundant with Ent2p; binds clathrin
via a clathrin-binding domain motif at C-terminus
14-3-3 protein, major isoform; binds proteins and DNA,
involved in regulation of many processes including exocytosis
and vesicle transport, Ras/MAPK signaling during
pseudohyphal development, rapamycin-sentitive signaling, and
others
and alpha cells
Histone H1, a linker histone required for nucleosome packaging
at restricted sites; suppresses DNA repair involving homologous
recombination; not required for telomeric silencing, basal
transcriptional repression, or efficient sporulation
URE2(0,3) ELA1(0,5) PDR16(0,0) CSL4(1,6) BNI4(12,1)
YNL234W YNL235C SIN4(6,8) YTP1(33,1) KEX2(1,3)
LAP3(0,0) NAR1(1,0) ZWF1(1,2)
Module genes
YML123C
PHO84
YJL012C
VTC4
YLR404W
None
YGR233C
PHO81
YCR098C
GIT1
YBR093C
PHO5
YAR071W
PHO11
YPL019C
VTC3
YLL052C
AQY2
YHR136C
SPL2
YDR281C
PHM6
YER072W
VTC1
YBR296C
PHO89
YHR215W
PHO12
YBR092C
PHO3
High-affinity inorganic phosphate (Pi) transporter and lowaffinity manganese transporter; regulated by Pho4p and Spt7p;
mutation confers resistance to arsenate; exit from the ER during
maturation requires Pho86p
Phosphate metabolism; transcription is regulated by PHO
system; polyphosphate synthetase (putative)
Cyclin-dependent kinase (CDK) inhibitor, regulates Pho80pPho85p and Pcl7p-Pho85p cyclin-CDK complexes in response
to phosphate levels; required for derepression of PHO5;
transcriptionally regulated by Pho4p and Pho2p
Plasma membrane permease, mediates uptake of the
phosphatidylinositol metabolite glycerophosphoinositol as a
source of the nutrients inositol and phosphate; expression and
transport rate are regulated by phosphate and inositol availability
One of three repressible acid phosphatases, a glycoprotein that is
transported to the cell surface by the secretory pathway; induced
by phosphate starvation and coordinately regulated by PHO4
and PHO2
transported to the cell surface by the secretory pathway; induced
by phosphate starvation and coordinately regulated by PHO4
and PHO2
Phosphate metabolism; transcription is regulated by PHO
system; polyphosphate synthetase (putative)
Water channel that mediates the transport of water across cell
membranes and may be involved in freeze tolerance; disrupted
by a stop codon in many S. cerevisiae strains
Protein with similarity to cyclin-dependent kinase inhibitors,
overproduction suppresses a plc1 null mutation; green
fluorescent protein (GFP)-fusion protein localizes to the
cytoplasm in a punctate pattern
Protein of unknown function, expression is regulated by
phosphate levels
Protein involved in vacuolar maintenance
Na+/Pi cotransporter, active in early growth phase; similar to
phosphate transporters of Neurospora crassa; transcription
regulated by inorganic phosphate concentrations and Pho4p
transported to the cell surface by the secretory pathway; nearly
identical to Pho11p; upregulated by phosphate starvation
Acid phosphatase, nearly identical to Pho5p; glycosylated;
transported to cell surface by secretory pathway; expression is
repressed by thiamine
(9) MODULE 10
YHR005C
GPA1
and alpha cells
Genotype regulators
UBP11(1,2) YKR099C-A BAS1(2,2) SKG1(5,0) SIR1(4,0)
FLO10(878,496)
M11_643655_643655
Module genes
YPR199C
ARR1
YPR198W
SGE1
YPR197C
(10) MODULE 11
None
YER040W
GLN3
YDR224C
HTB1
YDR264C
AKR1
YOR178C
GAC1
YKR099W
BAS1
YPR052C
NHP6A
YJL103C
Module genes
YDR425W
None
SNX41
YOR316C
COT1
YER055C
HIS1
YEL071W
DLD3
YBR249C
ARO4
Transcriptional activator of the bZIP family, required for
transcription of genes involved in resistance to arsenic
compounds
Member of drug-resistance protein family; multicopy suppressor
of gal11 null mutation
Transcriptional activator of genes regulated by nitrogen
catabolite repression (NCR), localization and activity regulated
by quality of nitrogen source
One of two nearly identical (see HTB2) histone H2B subtypes
required for chromatin assembly and chromosome function;
Rad6p-Bre1p-Lge1p mediated ubiquitination regulates
transcriptional activation, meiotic DSB formation and H3
methylation
Regulatory subunit for Glc7p (protein phosphatase I) for
glycogen synthesis; regulatory role also predicted for glucose
repression and ion homeostatis; potential Cdc28p substrate
Myb-related transcription factor involved in regulating basal and
induced expression of genes of the purine and histidine
biosynthesis pathways
Homologous to mammalian high mobility group proteins 1 and
2; functions redundantly with the highly homologous gene,
NHP6B; high-mobility group non-histone chromatin protein; 11kDa nonhistone chromosomal protein
Sorting nexin that mediates retrieval from endosomes
Vacuolar transporter that mediates zinc transport into the
vacuole; overexpression confers resistance to cobalt and
rhodium
ATP phosphoribosyltransferase, a hexameric enzyme, catalyzes
the first step in histidine biosynthesis; mutations cause histidine
auxotrophy and sensitivity to Cu, Co, and Ni salts; transcription
is regulated by general amino acid control
D-lactate dehydrogenase, part of the retrograde regulon which
consists of genes whose expression is stimulated by damage to
mitochondria and reduced in cells grown with glutamate as the
sole nitrogen source, located in the cytoplasm
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP)
YGL026C
YER090W
TRP5
TRP2
YNL229C
URE2
YKL033W-A
None
YHR137W
ARO9
YLL051C
FRE6
YPR005C
HAL1
YIL165C
None
YGR204W
ADE3
YBL029W
None
YLR034C
SMF3
YGR097W
ASK10
YCR099C
None
YGL162W
SUT1
YDR242W
AMD2
YDR234W
LYS4
YDR126W
SWF1
YDR408C
ADE8
YHL040C
ARN1
YAR015W
ADE1
YBR104W
YMC2
YDR531W
None
YIL094C
LYS12
synthase, catalyzes the first step in aromatic amino acid
biosynthesis and is feedback-inhibited by tyrosine
tryptophan synthetase
anthranilate synthase Component I
Nitrogen catabolite repression regulator that acts by inhibition of
GLN3 transcription in good nitrogen source; altered form of
Ure2p creates [URE3] prion
Aromatic aminotransferase, catalyzes the first step of
tryptophan, phenylalanine, and tyrosine catabolism
Putative ferric reductase with similarity to Fre2p; expression
induced by low iron levels
Cytoplasmic protein involved in halotolerance; decreases
intracellular Na+ (via Ena1p) and increases intracellular K+ by
decreasing efflux; expression repressed by Ssn6p-Tup1p and
Sko1p and induced by NaCl, KCl, and sorbitol through Gcn4p
Cytoplasmic trifunctional enzyme C1-tetrahydrofolate synthase,
involved in single carbon metabolism and required for
biosynthesis of purines, thymidylate, methionine, and histidine
Putative metal transporter, Nramp homolog, homolog of SMF1
and SMF2
Component of the RNA polymerase II holoenzyme,
phosphorylated in response to oxidative stress; has a role in
destruction of Ssn8p, which relieves repression of stressresponse genes
Involved in sterol uptake; hypoxic gene family involved in sterol
transport
Putative amidase
Homoaconitase, catalyzes the conversion of homocitrate to
homoisocitrate, which is a step in the lysine biosynthesis
pathway
Spore Wall Formation
Phosphoribosyl-glycinamide transformylase, catalyzes a step in
the 'de novo' purine nucleotide biosynthetic pathway
Transporter, member of the ARN family of transporters that
specifically recognize siderophore-iron chelates; responsible for
uptake of iron bound to ferrirubin, ferrirhodin, and related
siderophores
N-succinyl-5-aminoimidazole-4-carboxamide ribotide
(SAICAR) synthetase, required for 'de novo' purine nucleotide
biosynthesis; red pigment accumulates in mutant cells deprived
of adenine
Putative mitochondrial inner membrane transporter, member of
the mitochondrial carrier (MCF) family
Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial
enzyme required for the fourth step in the biosynthesis of lysine,
YJL087C
TRL1
YBL103C
RTG3
YNR065C
YSN1
YIL074C
SER33
YNL129W
NRK1
YPL212C
PUS1
YMR300C
ADE4
YHR122W
None
YKL106W
AAT1
YER061C
CEM1
YER045C
ACA1
YIL173W
VTH1
YMR120C
ADE17
YMR063W
YDR249C
RIM9
None
YOR363C
PIP2
YPR058W
YMC1
YMR019W
STB4
YDR380W
ARO10
YJL222W
VTH2
YCL009C
ILV6
in which homo-isocitrate is oxidatively decarboxylated to alphaketoadipate
tRNA ligase
Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription
factor that forms a complex with another bHLH/Zip protein,
Rtg1p, to activate the retrograde (RTG) and TOR pathways
Sortilin homolog, interacts with proteins of the endocytic
machinery
3-phosphoglycerate dehydrogenase, catalyzes the first step in
serine and glycine biosynthesis; isozyme of Ser3p
Nicotinamide riboside kinase, catalyzes the synthesis of
nicotinamide nucleotide (NMN) from nicotinamide riboside;
involved in a salvage pathway for NAD+ biosynthesis
Involved in tRNA biogenesis; intranuclear protein which
exhibits a nucleotide-specific intron-dependent tRNA
pseudouridine synthase activity
Phosphoribosylpyrophosphate amidotransferase (PRPPAT;
amidophosphoribosyltransferase), catalyzes first step of the 'de
novo' purine nucleotide biosynthetic pathway
Mitochondrial aspartate aminotransferase, catalyzes the
conversion of oxaloacetate to aspartate in aspartate and
asparagine biosynthesis
homology with beta-keto-acyl synthases; Protein homologous to
beta-keto-acyl synthase
Basic leucine zipper (bZIP) transcription factor of the
ATF/CREB family, may regulate transcription of genes involved
in utilization of non-optimal carbon sources
vps ten homolog; potential membrane glycoprotein with strong
similarity to Vth2 and Pep1/Vps10
Enzyme of 'de novo' purine biosynthesis containing both 5aminoimidazole-4-carboxamide ribonucleotide transformylase
and inosine monophosphate cyclohydrolase activities, isozyme
of Ade16p; ade16 ade17 mutants require adenine and histidine
Protein required for IME1 expression; involved in sporulation
peroxisome induction pathway 2 (PIP2); transcriptional activator
of peroxisome proliferation; may form heterodimer with Oaf1 to
activate oleate-inducible gene expression; activator of
peroxisome proliferation
Putative mitochondrial inner membrane transporter, member of
the mitochondrial carrier (MCF) family
Phenylpyruvate decarboxylase, catalyzes decarboxylation of
phenylpyruvate to phenylacetaldehyde, which is the first specific
step in the Ehrlich pathway
vps ten homolog; potential membrane glycoprotein with strong
similarity to Vth1 and Pep1
Regulatory subunit of acetolactate synthase, which catalyzes the
first step of branched-chain amino acid biosynthesis; enhances
activity of the Ilv2p catalytic subunit, localizes to mitochondria
YNR066C
None
YKR019C
IRS4
YBR035C
PDX3
YGL148W
ARO2
YLR303W
MET17
YDR426C
None
YER081W
SER3
YDL171C
GLT1
YLR004C
None
YNL240C
NAR1
YIL046W
MET30
(11) MODULE 12
YPL230W
None
YNL173C
MDG1
YPL230W
None
YBL084C
CDC27
YGL121C
GPG1
YPR052C
NHP6A
Protein involved in regulation of phosphatidylinositol 4,5bisphosphate concentrations; Irs4p and Tax4p bind and activate
the phosphatase Inp51p; mutation confers an increase in rDNA
silencing
Pyridoxine (pyridoxamine) phosphate oxidase, has homologs in
E. coli and Myxococcus xanthus; transcription is under the
general control of nitrogen metabolism
Bifunctional chorismate synthase and flavin reductase, catalyzes
the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP)
to form chorismate, which is a precursor to aromatic amino
acids
O-acetyl homoserine-O-acetyl serine sulfhydrylase, required for
sulfur amino acid synthesis
3-phosphoglycerate dehydrogenase, catalyzes the first step in
serine and glycine biosynthesis; isozyme of Ser33p
NAD(+)-dependent glutamate synthase (GOGAT), synthesizes
glutamate from glutamine and alpha-ketoglutarate; with Gln1p,
forms the secondary pathway for glutamate biosynthesis from
ammonia; expression regulated by nitrogen source
Component of the cytosolic iron-sulfur (FeS) protein assembly
machinery, required for maturation of cytosolic and nuclear FeS
proteins; homologous to human Narf (Nuclear prelamin A
Recognition Factor); Nuclear architecture related protein with
homology to human Narf (Nuclear prelamin A Recognition
Factor)
F-box protein containing five copies of the WD40 motif,
controls cell cycle function, sulfur metabolism, and methionine
biosynthesis as part of the ubiquitin ligase complex; interacts
with and regulates Met4p, localizes within the nucleus
Plasma membrane protein involved in G-protein mediated
pheromone signaling pathway; overproduction suppresses bem1
mutations
Subunit of the Anaphase-Promoting Complex/Cyclosome
(APC/C), which is a ubiquitin-protein ligase required for
degradation of anaphase inhibitors, including mitotic cyclins,
during the metaphase/anaphase transition
Proposed gamma subunit of the heterotrimeric G protein that
interacts with the receptor Grp1p; involved in regulation of
pseudohyphal growth; requires Gpb1p or Gpb2p to interact with
Gpa2p
Module genes
YBR116C
None
YPL134C
ODC1
YIL160C
POT1
YPR192W
AQY1
YGR256W
GND2
YMR102C
None
YKL093W
MBR1
YJL144W
None
YKL217W
JEN1
YMR086W
YDR034W-B
None
None
YKR009C
FOX2
YOR328W
PDR10
YNL194C
None
YJL066C
MPM1
YHR139C
SPS100
YPR012W
None
YHL032C
GUT1
YNL237W
YTP1
YAL053W
None
YLR174W
IDP2
Mitochondrial inner membrane transporter, exports 2-oxoadipate
and 2-oxoglutarate from the mitochondrial matrix to the cytosol
for use in lysine and glutamate biosynthesis and in lysine
catabolism
3-ketoacyl-CoA thiolase with broad chain length specifity,
cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA during
beta-oxidation of fatty acids
Water channel that mediates the transport of water across cell
membranes and may be involved in freeze tolerance
6-phosphogluconate dehydrogenase, decarboxylating; converts
6-phosphogluconate + NADP to ribulose-5-phosphate +
NADPH + CO2; 6-phosphogluconate dehydrogenase
Protein involved in mitochondrial functions and stress response;
overexpression suppresses growth defects of hap2, hap3, and
hap4 mutants
Lactate transporter, required for uptake of lactate and pyruvate;
expression is derepressed by transcriptional activator Cat8p
under nonfermentative growth conditions, and repressed in the
presence of glucose, fructose, and mannose
Multifunctional enzyme of the peroxisomal fatty acid betaoxidation pathway; has 3-hydroxyacyl-CoA dehydrogenase and
enoyl-CoA hydratase activities
ABC (ATP-binding cassette) membrane pump involved in the
pleiotropic drug resistance network, regulated by Pdr1p and
Pdr3p, similar to Pdr5p
Mitochondrial membrane protein of unknown function, contains
no hydrophobic stretches
involved in spore development; sporulation-specific wall
maturation protein
Glycerol kinase, converts glycerol to glycerol-3-phosphate;
glucose repression of expression is mediated by Adr1p and
Ino2p-Ino4p; derepression of expression on non-fermentable
carbon sources is mediated by Opi1p and Rsf1p
Probable type-III integral membrane protein of unknown
function, has regions of similarity to mitochondrial electron
transport proteins
Cytosolic NADP-specific isocitrate dehydrogenase, catalyzes
oxidation of isocitrate to alpha-ketoglutarate; levels are elevated
during growth on non-fermentable carbon sources and reduced
YHR096C
HXT5
YMR175W
SIP18
YER096W
SHC1
YNL117W
YDR536W
MLS1
STL1
YMR107W
SPG4
YKL163W
PIR3
YML054C
CYB2
YMR081C
ISF1
YDR534C
FIT1
YIL055C
None
YPR030W
CSR2
YOR348C
PUT4
YBR114W
RAD16
during growth on glucose
Hexose transporter with moderate affinity for glucose, may
function in accumulation of reserve carbohydrates during stress,
expression induced by a decrease in growth rate, contains an
extended N-terminal domain relative to other HXTs
Protein whose expression is induced by salt
Sporulation-specific activator of Chs3p (chitin synthase III),
required for the synthesis of the chitosan layer of ascospores;
has similarity to Skt5p, which activates Chs3p during vegetative
growth; transcriptionally induced at alkaline pH
carbon-catabolite sensitive malate synthase
sugar transporter-like protein
Protein required for survival at high temperature during
stationary phase
Protein containing tandem internal repeats
Expression is repressed by glucose and anaerobic conditions, is
induced by L-lactate and is regulated by GRR1, ROX3, HAP1,
HXK2 and CYC8; Cytochrome b2 [L--lactate cytochrome-c
oxidoreductase]
Serine-rich, hydrophilic protein with similarity to Mbr1p;
overexpression suppresses growth defects of hap2, hap3, and
hap4 mutants; expression is under glucose control; cotranscribed
with NAM7 in a cyp1 mutant
Mannoprotein that is incorporated into the cell wall via a
glycosylphosphatidylinositol (GPI) anchor, involved in the
retention of siderophore-iron in the cell wall
Nuclear protein with a potential regulatory role in utilization of
galactose and nonfermentable carbon sources; overproduction
suppresses the lethality at high temperature of a chs5 spa2
double null mutation; potential Cdc28p substrate
proline-specific permease (also capable of transporting alanine
and glycine); putative proline-specific permease
Protein that recognizes and binds damaged DNA in an ATPdependent manner (with Rad7p) during nucleotide excision
repair; subunit of Nucleotide Excision Repair Factor 4 (NEF4);
member of the SWI/SNF family
(12) MODULE 14
YGL121C
GPG1
YLL019C
KNS1
YJR122W
CAF17
Gpa2p
Nonessential putative protein kinase of unknown cellular role;
member of the LAMMER family of protein kinases, which are
serine/threonine kinases also capable of phosphorylating
tyrosine residues
YGR200C
ELP2
YNL023C
FAP1
YBL052C
Genotype regulators
SAS3
proteins
Elongator protein, part of the six-subunit RNA polymerase II
Elongator histone acetyltransferase complex; target of
Kluyveromyces lactis zymocin
Protein that binds to Fpr1p (FKBP12), conferring rapamycin
resistance by competing with rapamycin for Fpr1p binding; has
similarity to putative transcription factors, including D.
melanogaster shuttle craft and human NFX1
DCS1(0,4) YLR271W
M12_659357_674651
Module genes
YOL132W
GAS4
YDR271C
None
YPL194W
DDC1
YOR356W
None
YDR270W
CCC2
YJL100W
LSB6
YPR065W
ROX1
YJL049W
None
YKR046C
PET10
YLR231C
BNA5
YDL174C
DLD1
YAL039C
CYC3
YEL039C
CYC7
Putative 1,3-beta-glucanosyltransferase, has similarity to Gas1p;
localizes to the cell wall
DNA damage checkpoint protein, part of a PCNA-like complex
required for DNA damage response, required for pachytene
checkpoint to inhibit cell cycle in response to unrepaired
recombination intermediates; potential Cdc28p substrate
copper-transporting P-type ATPase with similarity to human
Menkes and Wilsons genes; Cu(2+)-transporting ATPase
Protein of unknown function; binds Las17p, which is a homolog
of human Wiskott-Aldrich Syndrome protein involved in actin
patch assembly and actin polymerization
Heme-dependent repressor of hypoxic genes; contains an HMG
domain that is responsible for DNA bending activity
Protein of unknown function that co-purifies with lipid particles;
expression pattern suggests a role in respiratory growth;
computational analysis of large-scale protein-protein interaction
data suggests a role in ATP/ADP exchange
Kynureninase, required for biosynthesis of nicotinic acid from
tryptophan via kynurenine pathway
D-lactate dehydrogenase, oxidizes D-lactate to pyruvate,
transcription is heme-dependent, repressed by glucose, and
derepressed in ethanol or lactate; located in the mitochondrial
inner membrane
Cytochrome c heme lyase (holocytochrome c synthase), attaches
heme to apo-Cyc1p in the mitochondrial intermembrane space;
human ortholog may have a role in microphthalmia with linear
skin defects (MLS)
Cytochrome c isoform 2, expressed under hypoxic conditions;
electron carrier of the mitochondrial intermembrane space that
transfers electrons from ubiquinone-cytochrome c
oxidoreductase to cytochrome c oxidase during cellular
respiration
YPR150W
YHR008C
YMR145C
YBL043W
None
SOD2
NDE1
ECM13
YNL328C
MDJ2
YJL048C
UBX6
YNL156C
NSG2
YMR220W
ERG8
YER141W
COX15
YBR183W
YPC1
Manganese-containing superoxide dismutase
None
Protein of the mitochondrial inner membrane; function partially
overlaps that of Mdj1p, which is a chaperone involved in folding
of mitochondrially synthesized proteins in the mitochondrial
matrix; member of the DnaJ family
UBX (ubiquitin regulatory X) domain-containing protein that
interacts with Cdc48p, transcription is repressed when cells are
grown in media containing inositol and choline
Protein of unknown function, potential homolog of mammalian
Insig 1
Phosphomevalonate kinase, an essential cytosolic enzyme that
acts in the biosynthesis of isoprenoids and sterols, including
ergosterol, from mevalonate
Protein required for the hydroxylation of heme O to form heme
A, which is an essential prosthetic group for cytochrome c
oxidase
Alkaline ceramidase that also has reverse (CoA-independent)
ceramide synthase activity, catalyzes both breakdown and
synthesis of phytoceramide; overexpression confers fumonisin
B1 resistance
(13) MODULE 15
YGL121C
GPG1
YJL141C
YAK1
YJL005W
CYR1
YCR091W
KIN82
YIL119C
RPI1
YPL026C
SKS1
YIL101C
XBP1
Gpa2p
Required for START A of cell cycle, and glucose and nitrogen
repression of sporulation; adenylate cyclase
Putative serine/threonine protein kinase, most similar to cyclic
nucleotide-dependent protein kinase subfamily and the protein
kinase C subfamily
Putative transcriptional regulator; overexpression suppresses the
heat shock sensitivity of wild-type RAS2 overexpression and
also suppresses the cell lysis defect of an mpk1 mutation
multicopy suppressor of snf3 and grr1 mutants; serine/threonine
protein kinase homologous to Ran1p
Transcriptional repressor that binds to promoter sequences of the
cyclin genes, CYS3, and SMF2; expression is induced by stress
or starvation during mitosis, and late in meiosis; member of the
Swi4p/Mbp1p family; potential Cdc28p substrate
Module genes
YGR019W
UGA1
YIL099W
SGA1
gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate
aminotransferase)
Intracellular sporulation-specific glucoamylase involved in
glycogen degradation; induced during starvation of a/a diploids
late in sporulation, but dispensable for sporulation
YLR252W
None
YDR070C
FMP16
YDR391C
None
YML070W
DAK1
YNL200C
YDL206W
YBR169C
None
None
SSE2
YPR184W
GDB1
YLR178C
TFS1
YGR088W
CTT1
YGR248W
SOL4
YHR104W
GRE3
YLR297W
YGR053C
None
None
YMR251W-A
HOR7
YML128C
MSC1
YER150W
SPI1
YDL048C
STP4
YKR049C
FMP46
YNL015W
PBI2
YNL305C
YGR201C
None
None
YPR160W
GPH1
YPR098C
None
YKL026C
GPX1
The authentic, non-tagged protein was localized to the
mitochondria
Dihydroxyacetone kinase, required for detoxification of
dihydroxyacetone (DHA); involved in stress adaptation
HSP70 family member, highly homologous to Sse1p
Glycogen debranching enzyme containing glucanotranferase and
alpha-1,6-amyloglucosidase activities, required for glycogen
degradation
Carboxypeptidase Y inhibitor; (putative) lipid binding protein;
supressor of a cdc25 mutation
Cytosolic catalase T, has a role in protection from oxidative
damage by hydrogen peroxide
Protein with similarity to Sol3p
Aldose reductase involved in methylglyoxal, d-xylose and
arabinose metabolism; stress induced (osmotic, ionic, oxidative,
heat shock, starvation and heavy metals); regulated by the HOG
pathway
Protein of unknown function; overexpression suppresses Ca2+
sensitivity of mutants lacking inositol phosphorylceramide
mannosyltransferases Csg1p and Csh1p; transcription is induced
under hyperosmotic stress and repressed by alpha factor
Protein of unknown function, green fluorescent protein (GFP)fusion protein localizes to the endoplasmic reticulum; msc1
mutants are defective in directing meiotic recombination events
to homologous chromatids
Protein with similarity to Sed1p; strongly expressed during
stationary phase, and trancription is dependent on Msn2p/Msn4p
Protein involved in pre-tRNA splicing and in uptake of
branched-chain amino acids
mitochondria
Cytosolic inhibitor of vacuolar proteinase B, required for
efficient vacuole inheritance; with thioredoxin forms protein
complex LMA1, which assists in priming SNARE molecules
and promotes vacuole fusion
Releases glucose-1-phosphate from glycogen; Glycogen
phosphorylase
Phospholipid hydroperoxide glutathione peroxidase induced by
glucose starvation that protects cells from phospholipid
hydroperoxides and nonphospholipid peroxides during oxidative
YGR194C
YLR177W
XKS1
None
YMR025W
CSI1
YLL019C
KNS1
YCL035C
GRX1
YBR117C
TKL2
YEL011W
GLC3
YKR076W
ECM4
YGR052W
FMP48
YPL223C
GRE1
YLL023C
YNR014W
None
None
YNL160W
YGP1
YNL274C
YPL123C
YKL091C
YMR090W
None
RNY1
None
None
YMR250W
GAD1
YDL130W-A
YDR074W
YKL151C
YBR285W
STF1
TPS2
None
None
YMR272C
SCS7
YPL230W
None
YOR178C
GAC1
stress
third enzyme in the xylose pathway; Xylulokinase
Subunit of the Cop9 signalosome, which is required for
deneddylation, or removal of the ubiquitin-like protein Rub1p
from Cdc53p (cullin); involved in adaptation to pheromone
signaling
tyrosine residues
Hydroperoxide and superoxide-radical responsive heat-stable
glutathione-dependent disulfide oxidoreductase with active site
cysteine pair; protects cells from oxidative damage
transketolase, homologous to tkl1
Glycogen branching enzyme, involved in glycogen
accumulation; green fluorescent protein (GFP)-fusion protein
localizes to the cytoplasm in a punctate pattern
Non-essential protein of unknown function; similar to Ygr154cp
mitochondria
Hydrophilin of unknown function; stress induced (osmotic,
ionic, oxidative, heat shock and heavy metals); regulated by the
HOG pathway
may be involved in cellular adaptations prior to stationary phase;
YGP1 encodes gp37, a glycoprotein synthesized in response to
nutrient limitation which is homologous to the sporulationspecific SPS100 gene
RNAse; member of the T(2) family of endoribonucleases
Glutamate decarboxylase, converts glutamate into gammaaminobutyric acid (GABA) during glutamate catabolism;
involved in response to oxidative stress
ATPase stabilizing factor
Trehalose-6-phosphate phosphatase
Required for the hydroxylation of the very long chain fatty acid
(VLCFA), located in the endoplasmic reticulum;
desaturase/hydroxylase enzyme
YJR096W
None
YIL136W
OM45
YOR289W
None
YJL161W
FMP33
YMR252C
None
YLR258W
GSY2
YDR275W
BSC2
YBR126C
TPS1
YBR230C
YPR117W
YAL061W
None
None
None
YLR270W
DCS1
YMR056C
AAC1
YKL142W
MRP8
YGL006W
PMC1
YPL087W
YDC1
YNL195C
YJL017W
None
None
YMR197C
VTI1
YDR171W
HSP42
YER053C
PIC2
YDR533C
HSP31
Protein of unknown function, major constituent of the
mitochondrial outer membrane; located on the outer (cytosolic)
face of the outer membrane
mitochondria
Glycogen synthase, similar to Gsy1p; expression induced by
glucose limitation, nitrogen starvation, heat shock, and
stationary phase; activity regulated by cAMP-dependent, Snf1p
and Pho85p kinases as well as by the Gac1p-Glc7p phosphatase
Protein of unknown function, ORF exhibits genomic
organization compatible with a translational readthroughdependent mode of expression
Probable regulator of glucose influx into the cell & into
glycolytic pathway, indirectly regulating glucose-induced
signalling (activation & inactivation) & initial step(s) of glucose
metabolism. Homologue of E. coli otsA protein; 56 kD synthase
subunit of trehalose-6-phosphate synthase/phosphatase complex
Non-essential hydrolase involved in mRNA decapping, may
function in a feedback mechanism to regulate deadenylation,
contains pyrophosphatase activity and a HIT (histidine triad)
motif; interacts with neutral trehalase Nth1p
Mitochondrial inner membrane ADP/ATP translocator,
exchanges cytosolic ADP for mitochondrially synthesized ATP;
Aac1p is a minor isoform while Pet9p is the major ADP/ATP
translocator
Putative mitochondrial ribosomal protein, has similarity to E.
coli ribosomal protein S2
May be involved in depleting cytosol of Ca2+ ions; putative
vacuolar Ca2+ ATPase
Yeast dihydro-ceramidase; alkaline dihydroceramidase with
minor reverse activity.
Involved in cis-Golgi membrane traffic; Vti1p is a v-SNARE
that interacts with two t-SNARES, Sed5p and Pep12p
Small cytosolic stress-induced chaperone that forms barrelshaped oligomers and suppresses the aggregation of non-native
proteins; oligomer dissociation is not required for function;
involved in cytoskeleton reorganization after heat shock
Mitochondrial phosphate carrier, imports inorganic phosphate
into mitochondria; functionally redundant with Mir1p but less
abundant than Mir1p under normal conditions; expression is
induced at high temperature
Possible chaperone and cysteine protease with similarity to E.
YDR453C
TSA2
YDL204W
RTN2
YHR080C
YBR286W
None
APE3
YDR032C
PST2
YMR169C
ALD3
YHR087W
YGR043C
None
None
YPL004C
LSP1
YMR181C
YMR196W
None
None
YML100W
TSL1
YER158C
None
YDL222C
FMP45
YNL055C
POR1
YOL048C
YHR016C
None
YSC84
YGR070W
ROM1
YFL030W
AGX1
YFL014W
HSP12
coli Hsp31 and S. cerevisiae Hsp32p, Hsp33p, and Sno4p;
member of the DJ-1/ThiJ/PfpI superfamily, which includes
human DJ-1 involved in Parkinson's disease; exists as a dimer
Thioredoxin-peroxidase, reduces H2O2 and alkyl
hydroperoxides with the use of hydrogens provided by
thioredoxin, thioredoxin reductase, and NADPH; provides
protection against oxidation systems that generate reactive
oxygen and sulfur species
reticulon gene member of the RTNLA (reticulon-like A)
subfamily
Vacuolar aminopeptidase Y, processed to mature form by Prb1p
Protein of unknown function with similarity to members of a
family of flavodoxin-like proteins; induced by oxidative stress in
a Yap1p dependent manner; GFP-fusion protein localizes to the
Aldehyde dehydrogenase that uses NAD+ as the preferred
coenzyme; expression is induced in response to heat shock,
oxidative, and osmotic stress
Long chain base-responsive inhibitor of protein kinases Phk1p
and Phk2p, acts along with Pil1p to down-regulate heat stress
resistance via regulation of the Pkc1p and Ypk1p pathways;
phosphorylated by Phk1p and Phk2p
123 kD regulatory subunit of trehalose-6-phosphate
synthase/phosphatase complex; homologous to TPS3 gene
product
mitochondria; cell cortex protein
Mitochondrial porin (voltage-dependent anion channel), outer
membrane protein required for the maintenance of
mitochondrial osmotic stability and mitochondrial membrane
permeability
SH3 domain in C-terminus
GDP/GTP exchange protein (GEP) for Rho1p; mutations are
synthetically lethal with mutations in rom2, which also encodes
a GEP
Alanine : glyoxylate aminotransferase, catalyzes the synthesis of
glycine from glyoxylate, which is one of three pathways for
glycine biosynthesis in yeast; has similairty to mammalian and
plant alanine : glyoxylate aminotransferases
Plasma membrane localized protein that protects membranes
from dessication; induced by heat shock, oxidative stress,
osmostress, stationary phase entry, glucose depletion, oleate and
alcohol; regulated by the HOG and Ras-Pka pathways
YNL115C
None
YIL155C
GUT2
YIL113W
YPR026W
YOL083W
SDP1
ATH1
None
YLR251W
SYM1
YGL037C
PNC1
YMR148W
YGL156W
None
AMS1
YER054C
GIP2
YMR041C
YMR105C
YPL186C
YIR016W
None
PGM2
UIP4
None
YMR297W
PRC1
YIL107C
PFK26
YGR044C
RME1
YOL085C
None
YIR038C
GTT1
YOL053C-A
None
YDL021W
GPM2
YDL223C
HBT1
YGR008C
YOL153C
YGR143W
STF2
None
SKN1
Mitochondrial glycerol-3-phosphate dehydrogenase; expression
is repressed by both glucose and cAMP and derepressed by nonfermentable carbon sources in a Snf1p, Rsf1p, Hap2/3/4/5
complex dependent manner
None
Vacuolar acid trehalase, required for trehalose utilization
Protein homologous to mammalian peroxisomal membrane
protein Mpv17; required for ethanol metabolismand induced by
heat shock; localized to the inner mitochondrial membrane
NAD(+) salvage pathway gene; pyrazinamidase and
nicotinamidase
vacuolar alpha mannosidase
Putative regulatory subunit of the protein phosphatase Glc7p,
proposed to be involved in glycogen metabolism; contains a
conserved motif (GVNK motif) that is also found in Gac1p,
Pig1p, and Pig2p
Phosphoglucomutase
Protein of unknown function
Vacuolar carboxypeptidase Y (proteinase C), involved in protein
degradation in the vacuole and required for full protein
degradation during sporulation
6-phosphofructo-2-kinase, inhibited by phosphoenolpyruvate
and sn-glycerol 3-phosphate, has negligible fructose-2,6bisphosphatase activity, transcriptional regulation involves
protein kinase A
mediates cell type control of sporulation; negatively regulates
IME1 and sporulation; zinc finger protein; negative regulator of
meiosis; directly repressed by a1-a2 regulator
ER associated glutathione S-transferase capable of
homodimerization; expression induced during the diauxic shift
and throughout stationary phase; functional overlap with Gtt2p,
Grx1p, and Grx2p
Similar to GPM1 (phosphoglycerate mutase); converts 3phosphoglycerate to 2-phosphoglycerate in glycolysis;
phosphoglycerate mutase, involved in glycolysis
Substrate of the Hub1p ubiquitin-like protein that localizes to
the shmoo tip (mating projection); mutants are defective for
mating projection formation, thereby implicating Hbt1p in
polarized cell morphogenesis
ATPase stabilizing factor
Involved in (1->6)-beta-glucan biosynthesis; encodes a predicted
YDR001C
NTH1
YPL154C
PEP4
YMR170C
ALD2
type II membrane protein highly homologous to Kre6p
Neutral trehalase, degrades trehalose; required for
thermotolerance and may mediate resistance to other cellular
stresses; may be phosphorylated by Cdc28p
Vacuolar aspartyl protease (proteinase A), required for the
posttranslational precursor maturation of vacuolar proteinases;
synthesized as a zymogen, self-activates
Cytosolic aldeyhde dehydrogenase that uses NAD+ as the
preferred coenzyme; expression is induced in response to high
osmotic stress
(14) MODULE 16
YIR017C
MET28
YFR009W
GCN20
YNL305C
None
YLR150W
STM1
YDR277C
MTH1
YGR123C
PPT1
YGR070W
ROM1
Module genes
YNL010W
None
YPR069C
SPE3
YMR012W
CLU1
YDL096C
None
YOR239W
ABP140
YER043C
SAH1
YER003C
PMI40
YMR186W
HSC82
YAL005C
SSA1
YOR198C
BFR1
Transcriptional activator in the Cbf1p-Met4p-Met28p complex,
participates in the regulation of sulfur metabolism
Positive regulator of the Gcn2p kinase activity, forms a complex
with Gcn1p; proposed to stimulate Gcn2p activation by an
uncharged tRNA
Protein that binds quadruplex nucleic acids; multicopy
suppressor of tom1 and pop2 mutations; acts with Cdc13p to
maintain telomere structure
Negative regulator of the glucose-sensing signal transduction
pathway, required for repression of transcription by Rgt1p;
interacts with Rgt1p and the Snf3p and Rgt2p glucose sensors;
phosphorylated by Yck1p, triggering Mth1p degradation
Protein serine/threonine phosphatase with similarity to human
phosphatase PP5; present in both the nucleus and cytoplasm;
expressed during logarithmic growth
a GEP
biosynthesis of spermidine; putrescine aminopropyltransferase
(spermidine synthase)
CLU1 is similar to the Dictyostelium cluA gene; translation
initiation factor eIF3 subunit
Nonessential protein that binds actin filaments and localizes to
actin patches and cables, has similarity to S-adenosylmethionine
(AdoMet)-dependent methyltransferases
Putative S-adenosyl-L-homocysteine hydrolase with a probable
role in S-adenosylhomocysteine catabolism and/or methionine
degradation
catalyzes the interconversion of fructose-6-P and mannose-6-P;
mannose-6-phosphate isomerase
constitutively expressed heat shock protein
Stress-seventy subfamily A; Heat shock protein of HSP70
family, cytoplasmic
Component of mRNP complexes associated with
YIL076W
SEC28
YAL004W
YLR301W
None
None
YOL141W
PPM2
YFL037W
TUB2
YNR016C
ACC1
YDL084W
SUB2
YGR087C
PDC6
YPL240C
HSP82
YLL024C
YJL105W
YHR042W
SSA2
SET4
NCP1
YMR307W
GAS1
YOR181W
LAS17
YER087C-A
None
YLR134W
PDC5
YMR215W
GAS3
YHR183W
GND1
YGL077C
HNM1
polyribosomes; implicated in secretion and nuclear segregation;
multicopy suppressor of BFA (Brefeldin A) sensitivity
Part of a heptameric protein complex that regulates retrograde
Golgi-to-ER protein traffic in eukaryotic cells; coatomer forms
the COP I vesicle coat whose functions are essential; epsilonCOP coatomer subunit Sec28p
Putative carboxyl methyl transferase, has similarity to Ppm1p
but biochemical activity not yet demonstrated
Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p)
to form tubulin dimer, which polymerizes to form microtubules
Acetyl-CoA carboxylase, biotin containing enzyme that
catalyzes the carboxylation of acetyl-CoA to form malonylCoA; required for de novo biosynthesis of long-chain fatty acids
Suppresses the cold-sensitive snRNP biogenesis brr1-1
mutation; RNA helicase
Minor isoform of pyruvate decarboxylase, key enzyme in
alcoholic fermentation, decarboxylates pyruvate to
acetaldehyde, regulation is glucose- and ethanol-dependent,
involved in amino acid catabolism
Cytoplasmic chaperone (Hsp90 family) required for pheromone
signaling and negative regulation of Hsf1p; docks with the
mitochondrial import receptor Tom70p for preprotein delivery;
interacts with co-chaperones Cns1p, Cpr6p, Cpr7p, and Sti1p
member of 70 kDa heat shock protein family
None
NADP-cytochrome P450 reductase
Beta-1.3-glucanosyltransferase, required for cell wall assembly;
localizes to the cell surface via a glycosylphosphatidylinositol
(GPI) anchor
Actin assembly factor, activates the Arp2/3 protein complex that
nucleates branched actin filaments; localizes with the Arp2/3
complex to actin patches; homolog of the human WiskottAldrich syndrome protein (WASP)
Minor isoform of pyruvate decarboxylase, key enzyme in
alcoholic fermentation, decarboxylates pyruvate to
acetaldehyde, regulation is glucose- and ethanol-dependent,
repressed by thiamine, involved in amino acid catabolism
Putative 1,3-beta-glucanosyltransferase, has similarity to Gas1p;
localizes to the cell wall
6-phosphogluconate dehydrogenase, decarboxylating; converts
6-phosphogluconate + NADP to ribulose-5-phosphate +
NADPH + CO2; Phosphogluconate Dehydrogenase
(Decarboxylating)
Choline transporter (permease) that also controls the uptake of
nitrogen mustard; expression is co-regulated with phospholipid
biosynthetic genes and negatively regulated by choline and myoinositol
YAL023C
PMT2
YAL038W
CDC19
YGR240C
PFK1
YJR105W
ADO1
YDR502C
SAM2
YJR143C
PMT4
YLR378C
(15) MODULE 17
SEC61
YMR001C
CDC5
YJR094C
IME1
YJL089W
SIP4
Transfers mannosyl residues from dolichyl phosphate-Dmannose to seryl and threonyl residues in proteins; acts in
complex with Pmt1p; dolichyl phosphate-D-mannose:protein OD-mannosyltransferase
Pyruvate kinase, functions as a homotetramer in glycolysis to
convert phosphoenolpyruvate to pyruvate, the input for aerobic
(TCA cycle) or anaerobic (glucose fermentation) respiration
Alpha subunit of heterooctameric phosphofructokinase involved
in glycolysis, indispensable for anaerobic growth, activated by
fructose-2,6-bisphosphate and AMP, mutation inhibits glucose
induction of cell cycle-related genes
adenosine kinase
S-adenosylmethionine synthetase, catalyzes transfer of the
adenosyl group of ATP to the sulfur atom of methionine; one of
two differentially regulated isozymes (Sam1p and Sam2p)
Transfers mannose residues from dolichyl phosphate-Dmannose to specific serine/threonine residues of proteins in the
secretory pathway; dolichyl phosphate-D-mannose:protein O-Dmannosyltransferase
membrane component of ER protein translocation apparatus
Polo-like kinase with similarity to Xenopus Plx1 and S. pombe
Plo1p; found at bud neck, nucleus and SPBs; has multiple
functions in mitosis and cytokinesis through phosphorylation of
substrates; may be a Cdc28p substrate
Master regulator of meiosis that is active only during meiotic
events, activates transcription of early meiotic genes through
interaction with Ume6p, degraded by the 26S proteasome
following phosphorylation by Ime2p
Possibly involved in Snf1p regulated transcriptional activation;
shows homology to DNA binding domain of Gal4p, has a
leucine zipper motif and acidic region; lexA-Sip4p activates
transcription
Module genes
YLR286C
CTS1
YJR160C
MPH3
YJR159W
SOR1
YDL247W
MPH2
YLR339C
YGL035C
None
MIG1
Endochitinase, required for cell separation after mitosis;
transcriptional activation during late G and early M cell cycle
phases is mediated by transcription factor Ace2p
Alpha-glucoside permease, transports maltose, maltotriose,
alpha-methylglucoside, and turanose; identical to Mph2p;
encoded in a subtelomeric position in a region likely to have
undergone duplication
Sorbitol dehydrogenase; expression is induced in the presence of
sorbitol
Alpha-glucoside permease, transports maltose, maltotriose,
alpha-methylglucoside, and turanose; identical to Mph3p;
encoded in a subtelomeric position in a region likely to have
undergone duplication
Transcription factor involved in glucose repression; C2H2 zinc
finger protein which resembles the mammalian Egr and Wilms
tumour proteins
YJL217W
None
YML093W
UTP14
YDR280W
RRP45
Nucleolar protein, component of the small subunit (SSU)
processome containing the U3 snoRNA that is involved in
processing of pre-18S rRNA
Ribosomal RNA Processing; Putative 3'->5' exoribonuclease;
component of exosome complex of 3'->5' exonucleases
(16) MODULE 18
YBL084C
CDC27
YDL064W
UBC9
YDR277C
MTH1
YMR036C
Module genes
MIH1
YNR033W
ABZ1
YDR193W
YBR277C
None
None
YPL046C
ELC1
YGL230C
YHR032W
None
None
YIR033W
MGA2
YJR156C
THI11
YML013C-A
YFR032C
YDL163W
None
None
None
YGR113W
DAM1
YJL091C
GWT1
SUMO-conjugating enzyme involved in the Smt3p conjugation
pathway; nuclear protein required for S- and M-phase cyclin
degradation and mitotic control; involved in proteolysis
mediated by the anaphase-promoting complex cyclosome
(APCC)
Para-aminobenzoate (PABA) synthase, has similarity to
Escherichia coli PABA synthase components PabA and PabB
Elongin C, forms heterodimer with Ela1p that participates in
transcription elongation; expression dramatically upregulated
during sporulation; widely conserved among eukaryotes
ER membrane protein involved, with its homolog Spt23p, in
regulation of OLE1 transcription; inactive ER form dimerizes
and one subunit is then activated by ubiquitin/proteasomedependent processing followed by nuclear targeting
Protein involved in synthesis of the thiamine precursor
hydroxymethylpyrimidine (HMP); member of a subtelomeric
gene family including THI5, THI11, THI12, and THI13
Component of the DASH complex, localized to intranuclear
spindles and spindle pole bodies; interacts with Duo1p and
Mps1p; key Ipl1p target for regulating kinetochore-microtubule
attachments
Protein involved in the inositol acylation of glucosaminyl
YKL076C
PSY1
phosphatidylinositol (GlcN-PI) to form
glucosaminyl(acyl)phosphatidylinositol (GlcN(acyl)PI), an
intermediate in the biosynthesis of glycosylphosphatidylinositol
(GPI) anchors
Dubious open reading frame, unlikely to encode a protein; not
conserved in closely related Saccharomyces species; 69% of
ORF overlaps the uncharacterized ORF YKL075C
(17) MODULE 20
YJL098W
SAP185
YIR026C
YVH1
YGL248W
PDE1
YPL203W
TPK2
YGL158W
YNR054C
YDR496C
Module genes
RCK1
ESF2
PUF6
YOR106W
VAM3
YNL303W
YDR339C
YDR161W
None
None
None
YDR179C
CSN9
YGL029W
CGR1
YPL266W
DIM1
YIL149C
MLP2
YKL110C
KTI12
YDR334W
SWR1
Protein that forms a complex with the Sit4p protein phosphatase
and is required for its function; member of a family of similar
proteins including Sap4p, Sap155p, and Sap190p
Low-affinity cyclic AMP phosphodiesterase, controls glucose
and intracellular acidification-induced cAMP signaling, target of
the cAMP-protein kinase A (PKA) pathway; glucose induces
transcription and inhibits translation
Involved in nutrient control of cell growth and division; cAMPdependent protein kinase catalytic subunit
Syntaxin-related protein; required for vacuolar assembly; PEP12
homolog; member of the syntaxin family of proteins; predicted
C-terminal TMD
Subunit of the Cop9 signalosome, which is required for
deneddylation, or removal of the ubiquitin-like protein Rub1p
from Cdc53p (cullin); involved in adaptation to pheromone
signaling
Coiled-coil protein that may contribute to compartmentalization
of nucleolar constituents; expression is growth-regulated
Essential 18S rRNA dimethylase, responsible for conserved
m6(2)Am6(2)A dimethylation in 3'-terminal loop of 18 S rRNA,
part of 90S and 40S pre-particles in nucleolus, involved in preribosomal RNA processing
Mlp proteins restrict telomere length by influencing the Rif1Tel1 pathway of telomerase regulation; also involved in the
translocation of macromolecules between the nucleoplasm and
the NPC; colied-coil protein (putative), similar to myosin and
TPR
Protein assoctiated with the RNA polymerase II Elongator
complex; involved in sensitivity to G1 arrest induced by
Kluyveromyces lactis toxin, zymocin
Swi2/Snf2-related ATPase, component of the SWR1 complex;
required for the incorporation of Htz1p into chromatin
YIL092W
None
YOL095C
HMI1
YDR527W
RBA50
YLR002C
NOC3
YIL064W
YHR066W
None
SSF1
YDR195W
REF2
YOR342C
None
YMR014W
BUD22
YDR110W
FOB1
YER161C
SPT2
YDL121C
None
YAL033W
POP5
YDR075W
PPH3
YML060W
OGG1
YDL166C
FAP7
YDL158C
None
YHR144C
DCD1
YLR003C
None
YNL186W
UBP10
YNL231C
PDR16
YGR272C
None
Mitochondrial inner membrane localized ATP-dependent DNA
helicase, required for the maintenance of the mitochondrial
genome; not required for mitochondrial transcription
Protein that forms a nuclear complex with Noc2p that binds to
66S ribosomal precursors to mediate their intranuclear transport;
also binds to chromatin to promote the association of DNA
replication factors and replication initiation
putative involvement in mating; homologous to Ssf2p
RNA-binding protein involved in the cleavage step of mRNA 3'end formation prior to polyadenylation; also involved in
snoRNA maturation
Protein involved in bud-site selection; diploid mutants display a
random budding pattern instead of the wild-type bipolar pattern
Nucleolar protein required for DNA replication fork blocking
and recombinational hotspot activities; binds to the replication
fork barrier site in the rDNA region; related to retroviral
integrases
Protein involved in negative regulation of transcription, exhibits
regulated interactions with both histones and SWI-SNF
components, has similarity to mammalian HMG1 proteins
Subunit of both RNase MRP, which cleaves pre-rRNA, and
nuclear RNase P, which cleaves tRNA precursors to generate
mature 5' ends
Catalytic subunit of protein phosphatase; involved in activation
of Gln3p, which is a transcription factor with a role in nitrogen
utilization
Mitochondrial glycosylase/lyase that specifically excises 7,8dihydro-8-oxoguanine residues located opposite cytosine or
thymine residues in DNA, repairs oxidative damage to
mitochondrial DNA
Essential nuclear protein, involved in the oxidative stress
response
Deaminase required for dCTP and dTTP synthesis; expression is
cell cycle regulated
Ubiquitin-specific protease that deubiquitinates ubiquitin-protein
moieties; may regulate silencing by acting on Sir4p; involved in
posttranscriptionally regulating Gap1p and possibly other
transporters; primarily located in the nucleus
Phosphatidylinositol transfer protein (PITP) controlled by the
multiple drug resistance regulator Pdr1p, localizes to lipid
particles and microsomes, controls levels of various lipids, may
regulate lipid synthesis, homologous to Pdr17p
YPL111W
YDL129W
CAR1
None
arginase
YDR045C
RPC11
YDR526C
YHL012W
YDR412W
None
None
None
YCL036W
GFD2
YNL150W
None
YHR184W
SSP1
Protein involved in the control of meiotic nuclear division and
spore formation
YOR051C
YGR251W
YPR143W
YNL191W
YHR041C
(18) MODULE 21
None
None
RRP15
None
SRB2
Essential protein involved in pre-rRNA processing
YPL153C
RAD53
YMR001C
CDC5
YDL101C
DUN1
RNA polymerase III subunit C11; mediates pol III RNA
cleavage activity and is important for termination of
transcription
Protein of unknown function, identified as a high-copy
suppressor of a dbp5 mutation
RNA polymerase II holoenzyme/mediator subunit
Protein kinase, required for cell-cycle arrest in response to DNA
damage; activated by trans autophosphorylation when
interacting with hyperphosphorylated Rad9p
repair
Module genes
YPL233W
NSL1
YPR194C
OPT2
YCL074W
YIL057C
None
None
YJL154C
VPS35
YCR022C
None
YML111W
BUL2
YPL164C
YML061C
MLH3
PIF1
Essential component of the MIND kinetochore complex (Mtw1p
Including Nnf1p-Nsl1p-Dsn1p) which joins kinetochore
subunits contacting DNA to those contacting microtubules;
required for accurate chromosome segregation
Oligopeptide transporter; member of the OPT family, with
potential orthologs in S. pombe and C. albicans
Protein involved in vacuolar sorting; retromer complex
component
a homologue of BUL1; (putative) ubiquitin-mediated protein
degradation
Mutl Homolog; MutL Homolog
involved in repair and recombination of mitochondrial DNA;
YHR056C
RSC30
YKL032C
IXR1
YJL179W
PFD1
YDR514C
None
YPL204W
HRR25
also plays a role in (nuclear) chromosomal telomere formation
and elongation; 5' to 3' DNA helicase
COX5b
Subunit of heterohexameric prefoldin, which binds cytosolic
chaperonin and transfers target proteins to it; involved in the
biogenesis of actin and of alpha- and gamma-tubulin
Similar to YCK1 and YCK2, two other casein kinase I isoforms;
found primarily in nucleus; may be involved in DNA-damage
repair; casein kinase I isoform
(19) MODULE 22
YFR009W
GCN20
YJL089W
SIP4
YOR337W
TEA1
YGR156W
PTI1
YDR283C
GCN2
YBR073W
RDH54
YJL098W
SAP185
uncharged tRNA
transcription
Mutants are defective in Ty1 Enhancer-mediated Activation;
Ty1 enhancer activator
Protein kinase, phosphorylates the alpha-subunit of translation
initiation factor eIF2 (Sui2p) in response to starvation; activated
by uncharged tRNAs and the Gcn1p-Gcn20p complex
genetic interaction with DMC1; Putative helicase similar to
RAD54
Module genes
YCR088W
ABP1
YPR035W
GLN1
YGL012W
ERG4
YFR006W
YFR044C
YCR013C
None
None
None
YDL160C
DHH1
Actin-binding protein of the cortical actin cytoskeleton,
important for activation of the Arp2/3 complex that plays a key
role actin in cytoskeleton organization
Glutamine synthetase (GS), synthesizes glutamine from
glutamate and ammonia; with Glt1p, forms the secondary
pathway for glutamate biosynthesis from ammonia; expression
regulated by nitrogen source and by amino acid limitation
C-24(28) sterol reductase, catalyzes the final step in ergosterol
biosynthesis; mutants are viable, but lack ergosterol
Cytoplasmic DExD/H-box helicase, stimulates mRNA
decapping, coordinates distinct steps in mRNA function and
YNL088W
TOP2
YKL153W
YIL123W
YCR012W
None
SIM1
PGK1
YHL030W
ECM29
YDL100C
ARR4
YML085C
TUB1
YKL182W
FAS1
YJR103W
URA8
YOL002C
IZH2
YNL058C
None
YMR076C
PDS5
YGL195W
GCN1
YER023W
PRO3
YNL057W
YLR460C
YMR323W
YJR116W
None
None
None
None
YDR388W
RVS167
YKL152C
GPM1
YPL231W
FAS2
YOR153W
PDR5
decay, interacts with both the decapping and deadenylase
complexes, may have a role in mRNA export and translation
Essential type II topoisomerase, catalyzes topology changes in
DNA via transient breakage and rejoining of phosphodiester
bonds in the DNA backbone; localizes to axial cores in meiosis
(putative) invovled in control of DNA replication
3-phosphoglycerate kinase
Major component of the proteasome; tethers the proteasome
core particle to the regulatory particle, and enhances the stability
of the proteasome
ATPase, involved in resistance to heat and metal stress, active as
a dimer; normally localized to the cytosol, but appears to
localize to late endosomes under stress conditions
Alpha-tubulin; associates with beta-tubulin (Tub2p) to form
tubulin dimer, which polymerizes to form microtubules
Beta subunit of fatty acid synthetase, which catalyzes the
synthesis of long-chain saturated fatty acids; contains
acetyltransacylase, dehydratase, enoyl reductase, malonyl
transacylase, and palmitoyl transacylase activities
Last step in pyrimidine biosynthesis pathway; CTP synthase
Membrane protein involved in zinc metabolism, member of the
four-protein IZH family, direct target of the Zap1p transcription
factor, expression induced by zinc deficiency and fatty acids,
deletion increases sensitivity to elevated zinc
Protein required for establishment and maintenance of sister
chromatid condensation and cohesion, colocalizes with cohesin
on chromosomes in an interdependent manner, may function as
a protein-protein interaction scaffold
uncharged tRNA
Delta 1-pyrroline-5-carboxylate reductase, catalyzes the last step
in proline biosythesis
BAR adaptor protein, subunit of a complex (Rvs161p-Rvs167p)
that regulates actin, endocytosis, and viability following
starvation or osmotic stress
converts 3-phosphoglycerate to 2-phosphoglycerate in
glycolysis; Phosphoglycerate mutase
Alpha subunit of fatty acid synthetase, which catalyzes the
synthesis of long-chain saturated fatty acids; contains betaketoacyl reductase and beta-ketoacyl synthase activities
Short-lived membrane ABC (ATP-binding cassette) transporter,
actively exports various drugs, expression regulated by Pdr1p;
also involved in steroid transport, cation resistance, and cellular
YDL185W
TFP1
YDR261C
EXG2
YGL173C
KEM1
YMR276W
DSK2
YBR127C
VMA2
YNL262W
POL2
YFL006W
YKL127W
YNL035C
None
PGM1
None
YGR180C
RNR4
YPL048W
CAM1
YGL060W
YBP2
YFL007W
BLM3
detoxification during exponential growth
Vacuolar ATPase V1 domain subunit A; protein precursor is
spliced to yield the extein Tfp1p and the intein Vde (PI-SceI),
which is a site-specific endonuclease
Exo-1,3-beta-glucanase, involved in cell wall beta-glucan
assembly; may be anchored to the plasma membrane via a
glycosylphosphatidylinositol (GPI) anchor
5'-3' exonuclease involved in mRNA decay, evolutionarily
conserved component of cytoplasmic processing (P) bodies,
plays a role in microtubule-mediated processes, filamentous
growth, and ribosomal RNA maturation
Nuclear-enriched ubiquitin-like polyubiquitin-binding protein,
required for spindle pole body (SPB) duplication and for transit
through the G2/M phase of the cell cycle, involved in
proteolysis, interacts with the proteasome
Vacuolar H+ ATPase regulatory subunit (subunit B) of the
catalytic (V1) sector
Catalytic subunit of DNA polymerase epsilon, one of the major
chromosomal DNA replication polymerases characterized by
processivity and proofreading exonuclease activity; also
involved in DNA synthesis during DNA repair
phosphoglucomutase, minor isoform
Ribonucleotide-diphosphate reductase (RNR), small subunit; the
RNR complex catalyzes the rate-limiting step in dNTP synthesis
and is regulated by DNA replication and DNA damage
checkpoint pathways via localization of the small subunits
Calcium and phospholipid binding protein homologous to
translation elongation factor 1-gamma (EF-1gamma)
Protein with a role in resistance to oxidative stress; has
similarity to Ybp1p, which is involved in regulation of the
transcription factor Yap1p via oxidation of specific cysteine
residues
Protein involved in assembly of proteasomal core particles in the
nucleus; required for normal resistance to bleomycin, may be
involved in protection against oxidative damage
(20) MODULE 23
YDR043C
NRG1
YPR070W
MED1
YDR496C
PUF6
YGL035C
MIG1
YJR122W
CAF17
Transcriptional repressor that recruits the Cyc8p-Tup1p complex
to promoters; mediates glucose repression and negatively
regulates a variety of processes including filamentous growth
and alkaline pH response
Subunit 1 of the Mediator complex essential for transcriptional
regulation
Transcription factor involved in glucose repression; C2H2 zinc
finger protein which resembles the mammalian Egr and Wilms
tumour proteins
Mitochondrial protein that interacts with Ccr4p in the two-
hybrid system; 3'-untranslated region contains a putative mRNA
proteins
Module genes
YDL027C
YMR173W-A
None
None
YMR302C
PRP12
YMR173W
DDR48
YLR121C
YPS3
YLR194C
YOR227W
YNL208W
None
None
None
YGR032W
GSC2
YGR250C
None
YBR182C
SMP1
YMR023C
MSS1
YMR280C
CAT8
YPL054W
YHL008C
YOR385W
YOR220W
LEE1
None
None
None
YNL093W
YPT53
YMR030W
RSF1
YMR191W
SPG5
YOR306C
MCH5
YKR061W
KTR2
YDL032W
None
Integral inner mitochondrial membrane protein with similarity to
exonucleases; prp12 mutants exhibit an increased rate of mt
DNA escape
DNA damage-responsive protein, expression is increased in
response to heat-shock stress or treatments that produce DNA
lesions; contains multiple repeats of the amino acid sequence
NNNDSYGS
Aspartic protease, attached to the plasma membrane via a
glycosylphosphatidylinositol (GPI) anchor
Catalytic subunit of 1,3-beta-glucan synthase, has similarity to
an alternate catalytic subunit, Fks1p (Gsc1p); Rho1p encodes
the regulatory subunit; involved in cell wall synthesis and
maintenance
Transcription factor of the MADS (Mcm1p, Agamous,
Deficiens, SRF) box family; closely related to RLM1; Probable
DNA-binding transcription factor, Homolog to SRF/SL-2
May play a part in mitochondrial translation; putative
mitochondrial GTPase
Zinc-cluster protein involved in activating gluconeogenic genes;
related to Gal4p
Involved in vacuolar protein sorting and endocytosis; GTPbinding protein of the rab family
Protein localized to both the nucleus and mitochondrion; mutant
displays decreased transcription of specific nuclear and
mitochondrial genes whose products are involved in respiratory
growth
Protein required for survival at high temperature during
stationary phase
Protein with similarity to mammalian monocarboxylate
permeases, which are involved in transport of monocarboxylic
acids across the plasma membrane; mutant is not deficient in
monocarboxylate transport
Mannosyltransferase involved in N-linked protein glycosylation;
member of the KRE2/MNT1 mannosyltransferase family
Protein of unknown function, has similarity to Pry1p and Pry3p
and to the plant PR-1 class of pathogen related proteins
Cell wall protein with similarity to glucanases; may play a role
in conjugation during mating based on mutant phenotype and its
regulation by Ste12p
Component of a complex containing the Tor2p kinase and other
proteins, which may have a role in regulation of cell growth
YKR013W
PRY2
YMR305C
SCW10
YMR068W
AVO2
YJR061W
YOL016C
YER130C
None
CMK2
None
Calmodulin-dependent protein kinase
YMR040W
YET2
Endoplasmic reticulum transmembrane protein, homolog of
human BAP31 protein
(21) MODULE 24
YJL056C
ZAP1
YGL254W
FZF1
zinc-finger domains
Transcription factor involved in sulfite resistance; contains five
zinc-fingers; activates SSU1 transcription
Module genes
YOL086C
ADH1
YMR303C
ADH2
YLR130C
ZRT2
YMR083W
ADH3
YDR235W
PRP42
YIL027C
KRE27
(22) MODULE 25
YBR125C
PTC4
YKL032C
IXR1
YLL019C
KNS1
Module genes
YFR012W
(23) MODULE 26
None
Alcohol dehydrogenase, involved in the production of certain
carboxylate esters
Glucose-repressible alcohol dehydrogenase II, involved in the
production of certain carboxylate esters
Low-affinity zinc transporter of the plasma membrane;
transcription is induced under low-zinc conditions by the Zap1p
transcription factor
Alcohol dehydrogenase isoenzyme III, shows a high affinity for
alcohols with a double bond conjugated to the alcohol group
U1 snRNP protein involved in splicing, required for U1 snRNP
biogenesis; contains multiple tetriatricopeptide repeats
Protein of unknown function; null mutant shows K1 killer toxin
resistance
COX5b
tyrosine residues
YGR123C
PPT1
YKL062W
MSN4
YOR337W
TEA1
Transcriptional activator related to Msn2p; activated in stress
conditions, which results in translocation from the cytoplasm to
the nucleus; binds DNA at stress response elements of
responsive genes, inducing gene expression
Genotype regulators
YAL042C-A ERV46(1,0) PTA1(4,0) YAL043C-A GCV3(3,4)
YAL044W-A YAL045C YAL046C SPC72(6,3) YAL047W-A
GEM1(1,1) YAL049C OAF1(6,1) YAL053W ACS1(2,7)
PEX22(3,3)
M1_51324_52943
Module genes
YAL049C
None
YGL205W
POX1
YOL147C
PEX11
YER015W
FAA2
YPR128C
(24) MODULE 27
ANT1
YJL089W
SIP4
YOL100W
PKH2
YDL064W
UBC9
YGR108W
CLB1
YDR296W
MHR1
Fatty-acyl coenzyme A oxidase, involved in the fatty acid betaoxidation pathway; localized to the peroxisomal matrix
May promote peroxisomal proliferation by participating in
peroxisomal elongation or fission or segregation of peroxisomes
to daughter cells; Peroxisomal membrane protein
Long chain fatty acyl-CoA synthetase; accepts a wider range of
acyl chain lengths than Faa1p, preferring C9:0-C13:0; involved
in the activation of endogenous pools of fatty acids
adenine nucleotide transporter; Adenine Nucleotide Transporter
transcription
(APCC)
Protein involved in mitochondrial homologous DNA
recombination and in transcription regulation; binds to
activation domains of acidic activators; presence in RNA pol II
holoenzyme may help recruit an Ssn3p-active form of the
Genotype regulators
RIP1(1,5) YEL025C SNU13(0,1) CUP5(0,0) YEL028W
BUD16(0,2) YEL030C-A ECM10(2,0) SPF1(1,0)
M5_99004_99004
Module genes
YJR036C
HUL4
Protein with similarity to hect domain E3 ubiquitin-protein
ligases, not essential for viability
YML020W
YLR377C
None
FBP1
YPL280W
HSP32
YBR250W
YNL295W
(25) MODULE 28
YDR496C
Genotype regulators
None
None
PUF6
Fructose-1,6-bisphosphatase, required for glucose metabolism
coli Hsp31 and S. cerevisiae Hsp31p, Hsp33p, and Sno4p;
member of the DJ-1/ThiJ/PfpI superfamily, which includes
human DJ-1 involved in Parkinson's disease
YLR149C-A STM1(0,0) PCD1(0,2) YLR152C ACS2(2,0)
RNH203(0,3) YLR154C-G YLR154C-H TAR1(0,0)
YLR154W-B YLR154W-C YLR154W-E YLR154W-F ASP31(193,529) YLR156C-A YLR156W ASP3-2(193,524)
YLR157C-C YLR157W-A YLR157W-C ASP3-3(193,529)
YLR159C-A YLR159W ASP3-4(193,529) YLR161W
YLR162W YLR162W-A YLR162W- MAS1(3,5) YLR163W-A
YLR164W PUS5(3,1) SEC10(7,11) RPS31(0,11) YLR168C
YLR169W APS1(1,2) YLR171W DPH5(0,5) YLR173W
IDP2(0,3) CBF5(1,2) RFX1(13,11) YLR177W TFS1(1,3)
YLR179C SAM1(0,10) VTA1(4,4)
M12_450041_508029
Module genes
YLR156W
None
YLR158C
ASP3-3
YLR161W
None
YLR155C
ASP3-1
YCL073C
None
YLR160C
ASP3-4
YLR159W
None
YLR157C
ASP3-2
Cell-wall L-asparaginase II, involved in asparagine catabolism;
expression is induced during nitrogen starvation; four copies of
ASP3 are present in the genome reference strain S288C
(26) MODULE 29
YJR094C
IME1
YDR277C
MTH1
Master regulator of meiosis that is active only during meiotic
events, activates transcription of early meiotic genes through
interaction with Ume6p, degraded by the 26S proteasome
following phosphorylation by Ime2p
Global transcription activator that acts in complex with Snf2p,
Snf5p, Snf6p, and Swi3p to assist gene-specific activators;
involved in the regulation of expression of many genes,
including ADH1, ADH2, GAL1, HO, INO1 and SUC2; Zincfinger transcription factor
YPL016W
SWI1
Module genes
YCR101C
YGR156W
YOR392W
None
PTI1
None
YGL091C
NBP35
NBP35 encodes an essential evolutionary conserved protein
with homology to bacterial partitioning ATPases; 35 kDa
nucleotide binding protein
YPR116W
YGR226C
YJL038C
None
None
None
YMR042W
ARG80
YPR014C
YIL060W
YHL037C
None
None
None
YOR173W
DCS2
YNL054W
VAC7
YPR067W
ISA2
YMR326C
(27) MODULE 30
YOL100W
None
PKH2
YJL005W
CYR1
YDR195W
REF2
YGL071W
RCS1
YPL016W
SWI1
Regulator of arginine-responsive genes with ARG81 and
ARG82; transcription factor
Non-essential protein containing a HIT (histidine triad) motif;
regulated by Msn2p, Msn4p, and the Ras-cAMP-cAPK
signalling pathway, transcript accumulates under glucose
limitation, similar to Dcs1p
Integral vacuolar membrane protein; may function to regulate
Fab1p kinase activity
Protein required for maturation of mitochondrial and cytosolic
Fe/S proteins, localizes to the mitochondrial intermembrane
space, overexpression of ISA2 suppresses grx5 mutations
snoRNA maturation
Transcription factor that binds the consensus site
PyPuCACCCPu, involved in iron homeostasis and cell size
regulation; activates the expression of target genes in response
to low-iron conditions
including ADH1, ADH2, GAL1, HO, INO1 and SUC2; Zinc-
YNL031C
HHT2
finger transcription factor
phosphorylation
Genotype regulators
FMP27(8,6) YLR455W YLR456W NBP1(2,5) YLR458W
GAB1(1,5) YLR460C PAU4(1,435)
M12_1056097_1056103
Module genes
YPR203W
YFL068W
None
None
YER190W
YRF1-2
YJL225C
YLR434C
None
None
YPL283C
YRF1-7
YLL067C
YEL076W-C
YEL077C
YIL177C
YFL066C
YLR463C
YBL109W
YDR544C
None
None
None
None
None
None
None
None
YLR466W
YRF1-4
YJR115W
YLR462W
YEL076C-A
YHR218W
YML133C
YBL111C
YHL049C
None
None
None
None
None
None
None
YNL339C
YRF1-6
YLR467W
YRF1-5
YEL075C
YNL338W
YHR219W
None
None
None
Helicase encoded by the Y' element of subtelomeric regions,
highly expressed in the mutants lacking the telomerase
component TLC1; potentially phosphorylated by Cdc28p
YER189W
YFL064C
YBL112C
None
None
None
YLR465C
BSC3
YPR202W
YEL074W
YFL067W
YLR464W
YLL066C
YHL050C
None
None
None
None
None
None
YDR545W
YRF1-1
YEL076C
YFL065C
YBL113C
None
None
None
YGR296W
YRF1-3
YLR465C overlaps the uncharacterized ORF YLR464W and
86% of YLR465C overlaps the verified gene YRF1-4
(28) MODULE 31
YGL229C
SAP4
YIL033C
BCY1
YDR523C
SPS1
YGR156W
PTI1
YMR179W
SPT21
YNL030W
HHF2
YKL109W
HAP4
Module genes
YMR325W
None
Protein required for function of the Sit4p protein phosphatase,
member of a family of similar proteins that form complexes with
Sit4p, including Sap155p, Sap185p, and Sap190p
Regulatory subunit of the cyclic AMP-dependent protein kinase
(PKA), a component of a signaling pathway that controls a
variety of cellular processes, including metabolism, cell cycle,
stress response, stationary phase, and sporulation
dispensable for mitosis, involved in middle/late stage of meiosis,
required for spore wall formation; serine/threonine kinase
homologous to Ste20p; expressed in middle/late meiosis
Protein required for normal transcription at several loci
including HTA2-HTB2 and HHF2-HHT2, but not required at
the other histone loci; functionally related to Spt10p
One of two identical histone H4 proteins (see also HHF1); core
histone required for chromatin assembly and chromosome
function; contributes to telomeric silencing; N-terminal domain
involved in maintaining genomic integrity
Subunit of the heme-activated, glucose-repressed
Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional
activator and global regulator of respiratory gene expression;
provides the principal activation function of the complex
YIL175W
YIR041W
None
None
YLR461W
PAU4
YDR542W
YLL064C
YIR040C
YGR294W
None
None
None
None
YJL223C
PAU1
YCR103C
YOR394W
YGL261C
YKL223W
YAL068C
YHL046C
YGL260W
YIL174W
YPL282C
YIL176C
YOL161C
(29) MODULE 33
None
None
None
None
None
None
None
None
None
None
None
YJL089W
SIP4
YCL026C-A
FRM2
YDL064W
UBC9
YPL026C
SKS1
YLR183C
TOS4
YDL101C
DUN1
Part of 23-member seripauperin multigene family encoded
mainly in subtelomeric regions, active during alcoholic
fermentation, regulated by anaerobiosis, negatively regulated by
oxygen, repressed by heme
transcription
Protein of unknown function, involved in the integration of lipid
signaling pathways with cellular homeostasis
(APCC)
Transcription factor that binds to a number of promoter regions,
particularly promoters of some genes involved in pheromone
response and cell cycle; potential Cdc28p substrate; expression
is induced in G1 by bound SBF
YJL098W
SAP185
Module genes
YDL218W
None
YOL156W
HXT11
YMR034C
YGR213C
None
RTA1
YCR021C
HSP30
YGR286C
BIO2
YLR445W
None
YLL063C
AYT1
YNL336W
COS1
YPL163C
SVS1
YIR043C
YAR060C
None
None
YIL085C
KTR7
YBR045C
GIP1
YNL289W
PCL1
YDR276C
PMP3
YDR540C
YML131W
None
None
YNL334C
SNO2
YGR295C
COS6
YMR206W
YPL272C
None
None
YJR161C
COS5
YDL248W
COS7
repair
Putative hexose transporter that is nearly identical to Hxt9p, has
similarity to major facilitator superfamily (MFS) transporters
and is involved in pleiotropic drug resistance
involved in 7-aminocholesterol resistance
Hydrophobic plasma membrane localized, stress-responsive
protein that negatively regulates the H(+)-ATPase Pma1p;
induced by heat shock, ethanol treatment, weak organic acid,
glucose limitation, and entry into stationary phase
Biotin synthase, catalyzes the conversion of dethiobiotin to
biotin, which is the last step of the biotin biosynthesis pathway;
complements E. coli bioB mutant
Acetyltransferase; catalyzes trichothecene 3-O-acetylation,
suggesting a possible role in trichothecene biosynthesis
Protein of unknown function, member of a family of conserved,
often subtelomerically-encoded proteins
Cell wall and vacuolar protein, required for wild-type resistance
to vanadate
Putative mannosyltransferase involved in protein glycosylation;
member of the KRE2/MNT1 mannosyltransferase family
Meiosis-specific protein proposed to be a regulatory subunit of
the protein phosphatase Glc7p, required for spore wall formation
and proper septin organization
Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into
the mitotic cell cycle and regulation of morphogenesis, localizes
to sites of polarized cell growth
plasma membrane protein involved in salt tolerance;
hypothetical transmembrane protein
Protein of unknown function, nearly identical to Sno3p;
expression is induced before the diauxic shift and also in the
absence of thiamin
YLR235C
YGR259C
YIR044C
None
None
None
YDR419W
RAD30
YBR302C
COS2
YLL047W
YIL120W
None
QDR1
YKL003C
MRP17
YEL049W
PAU2
YOL146W
PSF3
YML132W
COS3
YFL062W
COS4
YPL089C
RLM1
YPL281C
ERR2
YHL048W
COS8
YPR054W
SMK1
YNR074C
YPL096W
YEL070W
YDR400W
None
PNG1
DSF1
URH1
YIL131C
FKH1
YIL162W
SUC2
YGR189C
CRH1
YOR302W
None
YOR222W
ODC2
DNA polymerase eta, involved in the predominantly error-free
bypass replication of DNA lesions; homolog of human XPV and
bacterial DinB proteins
Quinidine Resistance; MFS-MDR transporter
Mitochondrial ribosomal protein of the small subunit; MRP17
exhibits genetic interactions with PET122, encoding a COX3specific translational activator
Subunit of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p),
which binds to DNA replication origins and facilitates assembly
of the DNA replication machinery
Protein involved in salt resistance; interacts with
sodium:hydrogen antiporter Nha1p; member of a family of
conserved, often subtelomerically-encoded proteins
serum response factor-like protein that may function
downstream of MPK1 (SLT2) MAP-kinase pathway; serum
response factor-like protein
Protein of unknown function, has similarity to enolases
Nuclear membrane protein, member of a family of conserved,
often subtelomerically-encoded proteins; regulation suggests a
potential role in the unfolded protein response
Mitogen-activated protein kinase required for spore
morphogenesis that is expressed as a middle sporulation-specific
gene
de-N-glycosylation enzyme; peptide:N-glycanase
None
uridine nucleosidase (uridine ribohydrolase); EC 3.2.2.3
Transcription factor of the forkhead family that regulates the cell
cycle and pseudohyphal growth; also involved in chromatin
silencing at HML and HMR
None
Putative glycosidase of the cell wall, may have a role in cell wall
architecture
Mitochondrial inner membrane transporter, exports 2-oxoadipate
and 2-oxoglutarate from the mitochondrial matrix to the cytosol
YNL014W
HEF3
YOL065C
INP54
for use in lysine and glutamate biosynthesis and in lysine
catabolism
Translational elongation factor EF-3; paralog of YEF3 and
member of the ABC superfamily; stimulates EF-1 alphadependent binding of aminoacyl-tRNA by the ribosome;
normally expressed in zinc deficient cells
Phosphatidylinositol 4,5-bisphosphate 5-phosphatase with a role
in secretion, localizes to the endoplasmic reticulum via the Cterminal tail; lacks the Sac1 domain and proline-rich region
found in the other 3 INP proteins
(30) MODULE 35
YIL033C
BCY1
YMR228W
MTF1
YDL170W
UGA3
YHR136C
SPL2
Mitochondrial RNA polymerase sigma-like specificity factor
required for promoter recognition, interacts with mitochondrial
core polymerase Rpo41p, imported into mitochondria via a
novel process requiring most of the Mtf1p sequence
Transcriptional activator necessary for gamma-aminobutyrate
(GABA)-dependent induction of GABA genes (such as UGA1,
UGA2, UGA4); zinc-finger transcription factor of the Zn(2)Cys(6) binuclear cluster domain type
Protein with similarity to cyclin-dependent kinase inhibitors,
overproduction suppresses a plc1 null mutation; green
fluorescent protein (GFP)-fusion protein localizes to the
Module genes
YLR308W
CDA2
YBR051W
YKL205W
None
LOS1
YPR179C
HDA3
YMR018W
None
YBR018C
GAL7
YMR265C
None
YPL209C
IPL1
YIR001C
SGN1
Required for proper formation of the ascospore wall; Chitin
Deacetylase
Nuclear pore protein involved in nuclear export of pre-tRNA
Subunit of a possibly tetrameric trichostatin A-sensitive class II
histone deacetylase complex that contains an Hda1p homodimer
and an Hda2p-Hda3p heterodimer; required for the activity of
the complex; has similarity to Hda2p
Galactose-1-phosphate uridyl transferase, synthesizes glucose-1phosphate and UDP-galactose from UDP-D-glucose and alphaD-galactose-1-phosphate in the second step of galactose
catabolism
Aurora kinase involved in regulating kinetochore-microtubule
attachments, associates with Sli5p, which stimulates Ipl1p
kinase activity and promotes its association with the mitotic
spindle, potential Cdc28p substrate
Cytoplasmic RNA-binding protein, contains an RNA
recognition motif (RRM); may have a role in mRNA translation,
as suggested by genetic interactions with genes encoding
proteins involved in translational initiation
(31) MODULE 36
YIR017C
MET28
YDR225W
HTA1
YMR019W
STB4
YJL187C
SWE1
YHR005C
GPA1
Protein kinase that regulates the G2/M transition by inhibition of
Cdc28p kinase activity; localizes to the nucleus and to the
daughter side of the mother-bud neck; homolog of S. pombe
Wee1p; potential Cdc28p substrate
and alpha cells
Genotype regulators
PMP3(0,3) MTH1(0,5) YDR278C RNH202(0,2) RRP45(0,0)
PHM6(0,2) YDR282C GCN2(2,0) DPP1(0,0) ZIP1(0,0)
YDR286C YDR287W NSE3(1,0) RTT103(2,0) YDR290W
YDR291W SRP101(1,1) SSD1(0,0)
M4_1022764_1039379
Module genes
YOR202W
HIS3
YIL164C
NIT1
YDL170W
UGA3
YDL066W
IDP1
YBR147W
None
YLR092W
SUL2
YMR062C
ECM40
YCL030C
HIS4
Imidazoleglycerol-phosphate dehydratase, catalyzes the sixth
step in histidine biosynthesis; mutations cause histidine
auxotrophy and sensitivity to Cu, Co, and Ni salts; transcription
is regulated by general amino acid control via Gcn4p
Nitrilase, member of the widely found nitrilase branch
(EC:3.5.5.1) of the nitrilase superfamily
Mitochondrial NADP-specific isocitrate dehydrogenase,
catalyzes the oxidation of isocitrate to alpha-ketoglutarate; not
required for mitochondrial respiration and may function to divert
alpha-ketoglutarate to biosynthetic processes
High affinity sulfate permease; sulfate uptake is mediated by
specific sulfate transporters Sul1p and Sul2p, which control the
concentration of endogenous activated sulfate intermediates
Mitochondrial ornithine acetyltransferase, catalyzes the fifth
step in arginine biosynthesis; also possesses acetylglutamate
synthase activity, regenerates acetylglutamate while forming
ornithine
Multifunctional enzyme containing phosphoribosyl-ATP
pyrophosphatase, phosphoribosyl-AMP cyclohydrolase, and
histidinol dehydrogenase activities; catalyzes the second, third,
ninth and tenth steps in histidine biosynthesis
YJR111C
None
YNL104C
LEU4
YFR030W
MET10
YBR047W
FMP23
YKL218C
SRY1
YJL088W
ARG3
YDR034C
LYS14
YOL140W
ARG8
YMR095C
SNO1
YGL125W
MET13
YGL117W
None
YOR303W
CPA1
YFR055W
None
YHR018C
ARG4
YDR354W
YOR203W
TRP4
None
YJR155W
AAD10
YOL118C
None
YMR094W
CTF13
YDR158W
HOM2
YOR184W
YHR017W
YJL089W
SER1
YSC83
SIP4
Alpha-isopropylmalate synthase (2-isopropylmalate synthase);
the main isozyme responsible for the first step in the leucine
biosynthesis pathway
Subunit alpha of assimilatory sulfite reductase, which is
responsible for the conversion of sulfite into sulfide
mitochondria
3-hydroxyaspartate dehydratase, deaminates L-threo-3hydroxyaspartate to form oxaloacetate and ammonia; required
for survival in the presence of hydroxyaspartate
Ornithine carbamoyltransferase (carbamoylphosphate:Lornithine carbamoyltransferase), catalyzes the sixth step in the
biosynthesis of the arginine precursor ornithine
Transcriptional activator involved in regulation of genes of the
lysine biosynthesis pathway; requires 2-aminoadipate
semialdehyde as co-inducer
Acetylornithine aminotransferase, catalyzes the fourth step in
the biosynthesis of the arginine precursor ornithine
Protein of unconfirmed function, involved in pyridoxine
metabolism; expression is induced during stationary phase;
forms a putative glutamine amidotransferase complex with
Snz1p, with Sno1p serving as the glutaminase
Isozyme of methylenetetrahydrofolate reductase, catalyzes the
reduction of 5,10-methylenetetrahydrofolate to 5methyltetrahydrofolate in the methionine biosynthesis pathway
Small subunit of carbamoyl phosphate synthetase, which
catalyzes a step in the synthesis of citrulline, an arginine
precursor; translationally regulated by an attenuator peptide
encoded by YOR302W within the CPA1 mRNA 5'-leader
Argininosuccinate lyase, catalyzes the final step in the arginine
anthranilate phosphoribosyl transferase
Putative aryl-alcohol dehydrogenase with similarity to P.
chrysosporium aryl-alcohol dehydrogenase; mutational analysis
has not yet revealed a physiological role
Subunit of the CBF3 complex, which binds to the CDE III
element of centromeres, bending the DNA upon binding, and
may be involved in sister chromatid cohesion during mitosis
Aspartic beta semi-aldehyde dehydrogenase, catalyzes the
second step in the common pathway for methionine and
threonine biosynthesis; expression regulated by Gcn4p and the
general control of amino acid synthesis
phosphoserine transaminase
similar to S. douglasii YSD83
YER052C
HOM3
YOR221C
MCT1
YIL003W
CFD1
YDL131W
LYS21
YNL036W
NCE103
YNL277W
MET2
YGL184C
STR3
YJR137C
ECM17
YFR025C
HIS2
YIL056W
YBR218C
None
PYC2
YPR145W
ASN1
YKL211C
TRP3
YGR267C
FOL2
YHR162W
None
YGL202W
ARO8
YDR106W
YGL114W
ARP10
None
YNR069C
BSC5
YJR109C
CPA2
transcription
Aspartate kinase (L-aspartate 4-P-transferase); cytoplasmic
enzyme that catalyzes the first step in the common pathway for
methionine and threonine biosynthesis; expression regulated by
Gcn4p and the general control of amino acid synthesis
Predicted malonyl-CoA:ACP transferase, putative component of
a type-II mitochondrial fatty acid synthase that produces
intermediates for phospholipid remodeling
Highly conserved, putative P-loop ATPase localized in the
cytoplasm; has a potential role in assembly of iron-sulfur
clusters in proteins
Homocitrate synthase isozyme, catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate, which
is the first step in the lysine biosynthesis pathway; highly similar
to the other isozyme, Lys20p
Protein with a carbonic anhydrase activity, involved in nonclassical protein export pathway
L-homoserine-O-acetyltransferase, catalyzes the conversion of
homoserine to O-acetyl homoserine which is the first step of the
methionine biosynthetic pathway
Cystathionine beta-lyase, converts cystathionine into
homocysteine
Sulfite reductase beta subunit, involved in amino acid
biosynthesis, transcription repressed by methionine
Histidinolphosphatase, catalyzes the eighth step in histidine
biosynthesis; mutations cause histidine auxotrophy and
sensitivity to Cu, Co, and Ni salts; transcription is regulated by
general amino acid control
converts pyruvate to oxaloacetate; pyruvate carboxylase
Asparagine synthetase, isozyme of Asn2p; catalyzes the
synthesis of L-asparagine from L-aspartate in the asparagine
biosynthetic pathway
anthranilate synthase Component II and indole-3-phosphate
(multifunctional enzyme)
GTP-cyclohydrolase I, catalyzes the first step in the folic acid
Aromatic aminotransferase, expression is regulated by general
control of amino acid biosynthesis
Actin-related protein
Protein of unknown function, ORF exhibits genomic
organization compatible with a translational readthroughdependent mode of expression
Large subunit of carbamoyl phosphate synthetase, which
catalyzes a step in the synthesis of citrulline, an arginine
precursor
YOR044W
None
YOR108W
LEU9
YJR148W
BAT2
YIL116W
HIS5
YDL198C
GGC1
YPR167C
MET16
YOL119C
MCH4
YKR069W
MET1
YJL213W
YGR239C
None
PEX21
YGR029W
ERV1
YGL224C
SDT1
YDR481C
PHO8
YDL025C
None
YOR337W
TEA1
YPR059C
None
YLR027C
AAT2
YBR145W
ADH5
YOL058W
ARG1
YLL027W
ISA1
Alpha-isopropylmalate synthase II (2-isopropylmalate synthase),
catalyzes the first step in the leucine biosynthesis pathway; the
minor isozyme, responsible for the residual alpha-IPMS activity
detected in a leu4 null mutant
Cytosolic branched-chain amino acid aminotransferase,
homolog of murine ECA39; highly expressed during stationary
phase and repressed during logarithmic phase
Histidinol-phosphate aminotransferase, catalyzes the seventh
step in histidine biosynthesis; responsive to general control of
amino acid biosynthesis; mutations cause histidine auxotrophy
and sensitivity to Cu, Co, and Ni salts
Mitochondrial GTP/GDP transporter, essential for mitochondrial
genome maintenance; has a role in mitochondrial iron transport;
member of the mitochondrial carrier family; (putative)
mitochondrial carrier protein
3'-phosphoadenylsulfate reductase, reduces 3'-phosphoadenylyl
sulfate to adenosine-3',5'-bisphosphate and free sulfite using
reduced thioredoxin as cosubstrate, involved in sulfate
assimilation and methionine metabolism
S-adenosyl-L-methionine uroporphyrinogen III transmethylase,
involved in sulfate assimilation, methionine metabolism, and
siroheme biosynthesis
Peroxin; Pex18p and Pex21p are partially functionally redundant
Flavin-linked sulfhydryl oxidase localized to the mitochondrial
intermembrane space, has a role in the maturation of cytosolic
iron-sulfur proteins; ortholog of human hepatopoietin (ALR)
Pyrimidine nucleotidase; overexpression suppresses the 6-AU
sensitivity of transcription elongation factor S-II, as well as
resistance to other pryimidine derivatives
Repressible alkaline phosphatase, a glycoprotein localized to the
vacuole; regulated by levels of inorganic phosphate and by a
system consisting of Pho4p, Pho9p, Pho80p, Pho81p and
Pho85p; dephosphorylates phosphotyrosyl peptides
Cytosolic aspartate aminotransferase, involved in nitrogen
metabolism; localizes to peroxisomes in oleate-grown cells
alcohol dehydrogenase isoenzyme V
Arginosuccinate synthetase, catalyzes the formation of Largininosuccinate from citrulline and L-aspartate in the arginine
biosynthesis pathway; potential Cdc28p substrate
Mitochondrial matrix protein involved in biogenesis of the iron-
sulfur (Fe/S) cluster of Fe/S proteins, isa1 deletion causes loss of
mitochondrial DNA and respiratory deficiency; depletion
reduces growth on nonfermentable carbon sources
YGL059W
None
YML116W
ATR1
YCR023C
None
YHR006W
STP2
YPL135W
ISU1
YMR097C
MTG1
YDR127W
ARO1
YOR130C
ORT1
YER128W
None
YLR267W
BOP2
YDR035W
ARO3
YPL188W
POS5
YDL054C
MCH1
YNL311C
YEL063C
None
CAN1
YOL064C
MET22
YHR071W
PCL5
Multidrug efflux pump of the major facilitator superfamily,
required for resistance to aminotriazole and 4-nitroquinoline-Noxide
Transcription factor, activated by proteolytic processing in
response to signals from the SPS sensor system for external
amino acids; activates transcription of amino acid permease
genes
Conserved protein of the mitochondrial matrix, performs a
scaffolding function during assembly of iron-sulfur clusters,
interacts physically and functionally with yeast frataxin (Yfh1p);
isu1 isu2 double mutant is inviable
Peripheral GTPase of the mitochondrial inner membrane,
essential for respiratory competence, likely functions in
assembly of the large ribosomal subunit, has homologs in plants
and animals
Pentafunctional arom protein, catalyzes steps 2 through 6 in the
biosynthesis of chorismate, which is a precursor to aromatic
amino acids
Ornithine transporter of the mitochondrial inner membrane,
exports ornithine from mitochondria as part of arginine
biosynthesis; human ortholog is associated with
hyperammonaemia-hyperornithinaemia-homocitrullinuria
(HHH) syndrome
Protein of unknown function, overproduction suppresses a pam1
slv3 double null mutation
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP)
synthase, catalyzes the first step in aromatic amino acid
biosynthesis and is feedback-inhibited by phenylalanine
Mitochondrial NADH kinase, phosphorylates NADH; also
phosphorylates NAD(+) with lower specificity; required for the
response to oxidative stress
arginine permease
Bisphosphate-3'-nucleotidase, involved in salt tolerance and
methionine biogenesis; dephosphorylates 3'-phosphoadenosine5'-phosphate and 3'-phosphoadenosine-5'-phosphosulfate,
intermediates of the sulfate assimilation pathway
Cyclin, interacts with Pho85p cyclin-dependent kinase (Cdk),
induced by Gcn4p at level of transcription, specifically required
for Gcn4p degradation, may be sensor of cellular protein
biosynthetic capacity
YMR096W
SNZ1
YJR130C
STR2
YER024W
YAT2
YER040W
GLN3
YDL057W
YBR043C
YFL028C
None
QDR3
CAF16
YCL026C-A
FRM2
YPL092W
SSU1
YGL180W
ATG1
YER069W
ARG5,6
YBR248C
HIS7
YBR256C
RIB5
YLR089C
YPL033C
YGL186C
YCR100C
YHR029C
ALT1
None
TPN1
None
None
YDR487C
RIB3
YER175C
YJL200C
TMT1
None
YDL182W
LYS20
YJL071W
ARG2
Snooze: stationary phase-induced gene family; involved in
cellular response to nutrient limitation and growth arrest;
encodes highly conserved 35 kDa protein that shows increased
expression after entry into stationary phase
Cystathionine gamma-synthase, converts cysteine into
cystathionine
Carnitine acetyltransferase; has similarity to Yat1p, which is a
carnitine acetyltransferase associated with the mitochondrial
outer membrane
Transcriptional activator of genes regulated by nitrogen
catabolite repression (NCR), localization and activity regulated
by quality of nitrogen source
Protein of unknown function, may have a role in drug resistance
CCR4 associated factor; ABC ATPase
putative sulfite pump; major facilitator superfamily protein
Protein serine/threonine kinase, required for autophagy and for
the cytoplasm-to-vacuole targeting (Cvt) pathway
Bifunctional enzyme with N-acetyl-gamma-glutamyl-phosphate
reductase and acetylglutamate kinase activities, catalyzes the
second and third steps in the biosynthesis of the arginine
precursor ornithine; forms a complex with Arg2p
Imidazole glycerol phosphate synthase (glutamine
amidotransferase:cyclase), catalyzes the fifth and sixth steps of
histidine biosynthesis and also produces 5-aminoimidazole-4carboxamide ribotide (AICAR), a purine precursor
Riboflavin synthase; catalyzes the last step of the riboflavin
putative alanine transaminase (glutamyc pyruvic transaminase)
Pyridoxine transporter
3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBP
synthase), required for riboflavin biosynthesis from ribulose-5phosphate, also has an unrelated function in mitochondrial
respiration
Trans-aconitate methyltransferase
Homocitrate synthase isozyme, catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate, which
is the first step in the lysine biosynthesis pathway; highly similar
to the other isozyme, Lys21p
Acetylglutamate synthase (glutamate N-acetyltransferase),
mitochondrial enzyme that catalyzes the first step in the
biosynthesis of the arginine precursor ornithine; forms a
complex with Arg5,6p
YPL250C
ICY2
YIR034C
LYS1
YGR288W
MAL13
(32) MODULE 37
YBL066C
SEF1
YPL075W
GCR1
YAL017W
PSK1
YJR127C
ZMS1
YJR147W
HMS2
YKR099W
BAS1
YFL031W
HAC1
Module genes
YML090W
YLR294C
YDR501W
None
None
PLM2
YBR039W
ATP3
YGL187C
COX4
YKL085W
MDH1
YJR080C
FMP26
YLR395C
COX8
YML002W
None
Protein that interacts with the cytoskeleton and is involved in
chromatin organization and nuclear transport, interacts
genetically with TCP1 and ICY1; potential Cdc28p substrate
Saccharopine dehydrogenase (NAD+, L-lysine-forming),
catalyzes the conversion of saccharopine to L-lysine, which is
the final step in the lysine biosynthesis pathway
MAL-activator protein, part of complex locus MAL1;
nonfunctional in genomic reference strain S288C
One of two (see also PSK2) PAS domain containing S/T protein
kinases; coordinately regulates protein synthesis and
carbohydrate metabolism and storage in response to a unknown
metabolite that reflects nutritional status
Zinc-finger protein that localizes to the nucleus, putative
transcriptional regulator of ALD6
Protein with similarity to heat shock transcription factors;
overexpression suppresses the pseudohyphal filamentation
defect of a diploid mep1 mep2 homozygous null mutant
bZIP transcription factor (ATF/CREB1 homolog) that regulates
the unfolded-protein response, via UPRE binding, and
membrane biogenesis; ER stress-induced splicing pathway
utilizing Ire1p, Trl1p and Ada5p facilitates efficient Hac1p
synthesis
Plasmid Maintenance; PLasmid Maintenance
Gamma subunit of the F1 sector of mitochondrial F1F0 ATP
synthase, which is a large, evolutionarily conserved enzyme
complex required for ATP synthesis
Subunit IV of cytochrome c oxidase, which is the terminal
member of the mitochondrial inner membrane electron transport
chain; N-terminal 25 residues of precursor are cleaved during
mitochondrial import
Mitochondrial malate dehydrogenase, catalyzes interconversion
of malate and oxaloacetate; involved in the tricarboxylic acid
(TCA) cycle
mitochondria
Subunit VIII of cytochrome c oxidase, which is the terminal
chain
YDR178W
SDH4
YNL037C
IDH1
YLR038C
COX12
YGR174C
CBP4
YGR182C
None
YBL030C
PET9
YLR295C
ATP14
YKL141W
SDH3
YKL109W
HAP4
YML120C
NDI1
YGL188C
None
YJR077C
MIR1
YPR020W
ATP20
YNL052W
COX5A
YMR256C
COX7
YFR033C
QCR6
YKR016W
FMP13
YEL024W
RIP1
Membrane anchor subunit of succinate dehydrogenase (Sdh1p,
Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate
to the transfer of electrons to ubiquinone
Subunit of mitochondrial NAD(+)-dependent isocitrate
dehydrogenase, which catalyzes the oxidation of isocitrate to
alpha-ketoglutarate in the TCA cycle
Subunit VIb of cytochrome c oxidase, which is the terminal
chain; required for assembly of fully active cytochrome c
oxidase but not required for activity after assembly
Essential for the expression and activity of ubiquinolcytochrome c reductase; ubiquinol--cytochrome-c reductase
assembly factor
Major ADP/ATP carrier of the mitochondrial inner membrane,
Pet9p and Sal1p have an overlapping function critical for
viability
Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase,
which is a large, evolutionarily conserved enzyme complex
required for ATP synthesis
Cytochrome b subunit of succinate dehydrogenase (Sdh1p,
NADH:ubiquinone oxidoreductase, transfers electrons from
NADH to ubiquinone in the respiratory chain but does not pump
protons, in contrast to the higher eukaryotic multisubunit
respiratory complex I which is absent in S. cerevisiae
Mitochondrial phosphate carrier, imports inorganic phosphate
into mitochondria; functionally redundant with Pic2p but more
abundant than Pic2 under normal conditions
Subunit g of the mitochondrial F1F0 ATP synthase, which is a
large enzyme complex required for ATP synthesis; associated
only with the dimeric form of ATP synthase
Subunit Va of cytochrome c oxidase, which is the terminal
chain; predominantly expressed during aerobic growth while its
isoform Vb (Cox5Bp) is expressed during anaerobic growth
Subunit VII of cytochrome c oxidase, which is the terminal
chain
ubiquinol-cytochrome c oxidoreductase subunit 6 (17 kDa)
mitochondria
oxidizes ubiquinol at center P in the protonmotive Q cycle
mechanism, transferring one electron to cytochrome c1 and
YDR148C
KGD2
YML081C-A
ATP18
YGR183C
QCR9
YBR085W
AAC3
YPL271W
ATP15
YGL191W
COX13
YMR002W
None
YKL148C
SDH1
YLR299W
ECM38
YBL099W
ATP1
YHR001W-A
QCR10
YLR168C
YJL166W
YJR120W
YOR065W
None
QCR8
None
CYT1
YDL004W
ATP16
YIL125W
KGD1
YJL103C
None
YDL181W
INH1
generating a low-potential ubisemiquinone anion which reduces
the low-potential cytochrome b-566 heme group; Rieske ironsulfur protein of the mitochondrial cytochrome bc1 complex
Dihydrolipoyl transsuccinylase, a component of the
mitochondrial alpha-ketoglutarate dehydrogenase complex,
which catalyzes a step in the tricarboxylic acid (TCA) cycle, the
oxidative decarboxylation of alpha-ketoglutarate to succinylCoA
Subunit of the mitochondrial F1F0 ATP synthase, which is a
large enzyme complex required for ATP synthesis; termed
subunit I or subunit j; does not correspond to known ATP
synthase subunits in other organisms
7.3 kDa subunit 9 of the ubiquinol cytochrome c oxidoreductase
complex
Mitochondrial inner membrane ADP/ATP translocator,
expressed under anaerobic conditions; similar to Pet9p and
Aac1p; has roles in maintenance of viability and in respiration
Epsilon subunit of the F1 sector of mitochondrial F1F0 ATP
Subunit VIa of cytochrome c oxidase, which is the terminal
chain; not essential for cytochrome c oxidase activity but may
modulate activity in response to ATP
Flavoprotein subunit of succinate dehydrogenase (Sdh1p,
Gamma-glutamyltranspeptidase, major glutathione-degrading
enzyme; expression induced mainly by nitrogen starvation
Alpha subunit of the F1 sector of mitochondrial F1F0 ATP
8.5 kDa subunit of the ubiqunol-cytochrome c oxidoreductase
complex
Ubiquinol cytochrome-c reductase subunit 8 (11 kDa protein)
Cytochrome c1
Delta subunit of the central stalk of mitochondrial F1F0 ATP
Component of the mitochondrial alpha-ketoglutarate
dehydrogenase complex, which catalyzes a key step in the
tricarboxylic acid (TCA) cycle, the oxidative decarboxylation of
alpha-ketoglutarate to form succinyl-CoA
Protein that inhibits ATP hydrolysis by the F1F0-ATP synthase,
inhibitory function is enhanced by stabilizing proteins Stf1p and
YLR304C
ACO1
YKL016C
ATP7
YLL041C
SDH2
YDR298C
ATP5
YDR322C-A
TIM11
YBL100C
None
YHR051W
COX6
YJL102W
YPR191W
MEF2
QCR2
YCL058C
FYV5
YJR121W
ATP2
YDR377W
ATP17
YDL067C
COX9
YBL045C
COR1
YPL078C
ATP4
Stf2p; has similarity to Stf1p and both Inh1p and Stf1p exhibit
the potential to form coiled-coil structures
Mitochondrial aconitase, required for the tricarboxylic acid
(TCA) cycle; mutation leads to glutamate auxotrophy
Subunit d of the stator stalk of mitochondrial F1F0 ATP
Iron-sulfur protein subunit of succinate dehydrogenase (Sdh1p,
Subunit 5 of the stator stalk of mitochondrial F1F0 ATP
complex required for ATP synthesis; homologous to bovine
subunit OSCP (oligomycin sensitivity-conferring protein)
Protein associated with mitochondrial ATP synthase; essential
for dimeric state of ATP synthase. ; subunit e of mitochondrial
F1F0-ATPase
Subunit VI of cytochrome c oxidase, which is the terminal
chain; expression is regulated by oxygen levels
mitochondrial elongation factor G-like protein
40 kDa ubiquinol cytochrome-c reductase core protein 2
Protein of unknown function, required for survival upon
exposure to K1 killer toxin; involved in ion homeostasis
Beta subunit of the F1 sector of mitochondrial F1F0 ATP
Subunit f of the F0 sector of mitochondrial F1F0 ATP synthase,
which is a large, evolutionarily conserved enzyme complex
required for ATP synthesis
Subunit VIIa of cytochrome c oxidase, which is the terminal
chain
Core subunit of the ubiquinol-cytochrome c reductase complex
(bc1 complex), which is a component of the mitochondrial inner
membrane electron transport chain
Subunit b of the stator stalk of mitochondrial F1F0 ATP
(33) MODULE 38
YOR304W
ISW2
YIL147C
SLN1
Member of the imitation-switch (ISWI) class of ATP-dependent
chromatin remodeling complexes; ATPase component that, with
Itc1p, forms a complex required for repression of a-specific
genes, INO1, and early meiotic genes during mitotic growth
Histidine kinase osmosensor that regulates a MAP kinase
cascade; transmembrane protein with an intracellular kinase
domain that signals to Ypd1p and Ssk1p, thereby forming a
phosphorelay system similar to bacterial two-component
regulators
YIL147C
SLN1
YIL147C
SLN1
YOR230W
WTM1
YKL062W
MSN4
regulators
regulators
Genotype regulators
ARF1(0,3) YDL193W SNF3(12,2) SEC31(6,4) YDL196W
ASF2(9,4) GGC1(0,4) YDL199C MGT1(3,0) TRM8(0,4)
MRPL11(0,4) YDL203C RTN2(0,5) HEM3(0,5) YDL206W
GLE1(4,5) NHP2(1,2) CWC2(1,2) UGA4(1,9) YDL211C
SHR3(1,3) NOP6(0,3)
M4_85846_106892
Module genes
YFL002W-A
YBL005W-B
YBL101W-B
YMR046C
YLR035C-A
YHR214C-B
YFL035C-A
YDL230W
YBL107W-A
YMR050C
None
None
None
None
None
None
None
PTP1
None
None
YDR283C
GCN2
YCR018C-A
YJR026W
None
None
YEL069C
HXT13
YLR334C
YMR158C-B
None
None
YCR032W
BPH1
YDR170W-A
YDR034C-A
None
None
Protein of unknown function with similarity to hexose
transporter family members, expression is induced by low levels
of glucose and repressed by high levels of glucose
Protein homologous to human Chediak-Higashi syndrome
protein and murine beige gene, which are implicated in disease
syndromes due to defective lysosomal trafficking
YER160C
YML039W
YJR039W
YAL001C
YER138W-A
YJR027W
YBR013C
YKL215C
YBR012W-B
YBL005W-A
None
None
None
TFC3
None
None
None
None
None
None
YML049C
RSE1
YMR046W-A
None
YMR308C
PSE1
YAR009C
YGR122C-A
YCL019W
None
None
None
YDL246C
SOR2
YIL015C-A
None
YHR102W
KIC1
YML040W
YOL106W
YJL007C
None
None
None
YMR176W
ECM5
YER138C
YMR045C
YML045W
YJR029W
YAR029W
None
None
None
None
None
YMR128W
ECM16
YDL243C
AAD4
YAL002W
VPS8
transcription factor tau (TFIIIC) subunit 138
RNA splicing and ER to Golgi transport; involved in secretion
and RNA splicing
Karyopherin/importin that interacts with the nuclear pore
complex; acts as the nuclear import receptor for specific
proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p
Protein of unknown function, computational analysis of largescale protein-protein interaction data suggests a possible role in
fructose or mannose metabolism
Protein kinase of the PAK/Ste20 kinase family, required for cell
integrity possibly through regulating 1,6-beta-glucan levels in
the wall; physically interacts with Cdc31p (centrin), which is a
component of the spindle pole body
Non-essential protein of unknown function, contains ATP/GTPbinding site motif A; null mutant exhibits cellular volume up to
four times greater than wild-type, also large drooping buds with
elongated necks
Essential DEAH-box ATP-dependent RNA helicase specific to
the U3 snoRNP, predominantly nucleolar in distribution,
required for 18S rRNA synthesis
chrysosporium aryl-alcohol dehydrogenase, involved in the
oxidative stress response
involved in vacuolar protein sorting; required for localization
and trafficking of the CPY sorting receptor; Vps8p is a
YOL051W
GAL11
YGL094C
PAN2
YHL045W
YCL069W
YLR225C
YPR002C-A
(34) MODULE 39
None
None
None
None
YBR274W
CHK1
YHL027W
RIM101
YAL017W
PSK1
YDR034C
LYS14
YDR496C
PUF6
YNL180C
RHO5
membrane-associated hydrophilic protein which contains a Cterminal cysteine-rich region that conforms to the H2 variant of
the RING finger Zn2+ binding motif.
Component of the Mediator complex; interacts with RNA
polymerase II and the general transcription factors to form the
RNA polymerase II holoenzyme; affects transcription by acting
as target of activators and repressors
Essential subunit of the Pan2p-Pan3p poly(A)-ribonuclease
complex, which acts to control poly(A) tail length and regulate
the stoichiometry and activity of postreplication repair
complexes
Transcriptional activator required for entry into meiosis, has
similarity to the Aspergillus Phenotype-response regulator PacC
and the Yarrowia proteinase YlRim1010p; Meiotic regulatory
protein; Cys-His zinc fingers
Transcriptional activator involved in regulation of genes of the
lysine biosynthesis pathway; requires 2-aminoadipate
semialdehyde as co-inducer
Non-essential small GTPase of the Rho/Rac subfamily of Raslike proteins, likely involved in protein kinase C (Pkc1p)dependent signal transduction pathway that controls cell
integrity
Module genes
YBR140C
IRA1
YBR036C
CSG2
YBR171W
SEC66
YBR235W
None
YBL101C
ECM21
YBL094C
None
GTPase-activating protein that negatively regulates RAS by
converting it from the GTP- to the GDP-bound inactive form,
required for reducing cAMP levels under nutrient limiting
conditions, mediates membrane association of adenylate cyclase
Endoplasmic reticulum membrane protein, required for
mannosylation of inositolphosphorylceramide and for growth at
high calcium concentrations
glycoprotein complexed with Sec62p and Sec63p in the Sec63
complex, an integral endoplasmic reticulum membrane protein
complex required for translocation of presecretory proteins
Non-essential protein of unknown function; promoter contains
several Gcn4p binding elements
YBR008C
FLR1
YBR151W
APD1
YBR071W
YBL066C
None
SEF1
YBL074C
AAR2
YBL089W
AVT5
YBR173C
UMP1
YBR096W
None
YBR221C
PDB1
YBL022C
PIM1
YBR136W
MEC1
YBR297W
MAL33
YBL098W
BNA4
YBR108W
YBR212W
None
NGR1
YBR086C
IST2
YBR293W
None
YBL047C
EDE1
YDR264C
AKR1
YBR138C
None
YBR170C
NPL4
Plasma membrane multidrug transporter, member of the major
facilitator superfamily; involved in efflux of fluconazole,
diazaborine, benomyl, methotrexate, and other drugs
Protein of unknown function, required for normal localization of
actin patches and for normal tolerance of sodium ions and
hydrogen peroxide; localizes to both cytoplasm and nucleus
Component of the U5 snRNP, required for splicing of U3
precursors; originally described as a splicing factor specifically
required for splicing pre-mRNA of the MATa1 cistron
Putative transporter, member of a family of seven S. cerevisiae
genes (AVT1-7) related to vesicular GABA-glycine transporters
Involved in ubiquitin-mediated proteolysis; 20S proteasome
maturation factor
E1 beta subunit of the pyruvate dehydrogenase (PDH) complex,
which is an evolutionarily-conserved multi-protein complex
found in mitochondria
mitochondrial ATP-dependent protease
Central regulator of the Mec1p/Tel1p signaling network;
required for mitotic growth, DNA repair and mitotic
recombination, regulates phosphorylation of Rad53p, required
for dmc1 arrest and meiotic recombination; similar to
phosphatidylinositol(PI)3-kinases required for DNA damage
induced checkpoint responses in G1, S/M, intra S, and G2/M in
mitosis
Kynurenine 3-mono oxygenase, required for biosynthesis of
nicotinic acid from tryptophan via kynurenine pathway
Plasma membrane protein that may be involved in
osmotolerance, localizes to the mother cell in small-budded cells
and to the bud in medium- and large-budded cells; mRNA is
transported to the bud tip by an actomysin-driven process
Key endocytic protein involved in a network of interactions with
other endocytic proteins, binds membranes in a ubiquitindependent manner, may also bind ubiquitinated membraneassociated proteins
Endoplasmic reticulum and nuclear membrane protein, forms a
complex with Cdc48p and Ufd1p that recognizes ubiquitinated
proteins in the endoplasmic reticulum and delivers them to the
proteasome for degradation
YBR234C
ARC40
YBR016W
YBL107C
None
None
YPL148C
PPT2
YBR020W
GAL1
YBR222C
PCS60
YBL007C
SLA1
YBR291C
CTP1
YBR225W
None
YBL084C
CDC27
YBL102W
YOR275C
SFT2
RIM20
YBR041W
FAT1
YBR059C
AKL1
YBR223C
YBR055C
TDP1
PRP6
YBR005W
RCR1
YBR019C
GAL10
YBR211C
AME1
YJR037W
None
YBR111C
YSA1
YBR007C
DSF2
YBR038W
CHS2
Arp2/3 complex subunit, 40 kilodalton; component of
Arp2/Arp3 protein complex
Phosphopantetheine:protein transferase (PPTase), activates
mitochondrial acyl carrier protein (Acp1p) by
phosphopantetheinylation
Galactokinase, phosphorylates alpha-D-galactose to alpha-Dgalactose-1-phosphate in the first step of galactose catabolism;
expression regulated by Gal4p
Peroxisomal AMP-binding protein, localizes to both the
peroxisomal peripheral membrane and matrix, expression is
highly inducible by oleic acid, similar to E. coli long chain acylCoA synthetase
Cytoskeletal protein binding protein required for assembly of the
cortical actin cytoskeleton; contains 3 SH3 domains; interacts
with proteins regulating actin dynamics and with proteins
required for endocytosis
Mitochondrial inner membrane citrate transporter, member of
the mitochondrial carrier family
similar to mammalian syntaxin 5
Regulator of IME2
Fatty acid transporter and very long-chain fatty acyl-CoA
synthetase, may form a complex with Faa1p or Faa4p that
imports and activates exogenous fatty acids
Serine-threonine protein kinase, member (with Ark1p and
Prk1p) of the Ark kinase family
Tyrosine-DNA Phosphodiesterase
Splicing factor, component of the U4/U6-U5 snRNP complex
Endoplasmic reticulum membrane protein whose
overproduction confers resistance to Congo Red
UDP-glucose-4-epimerase, catalyzes the interconversion of
UDP-galactose and UDP-D-glucose in galactose metabolism;
also catalyzes the conversion of alpha-D-glucose or alpha-Dgalactose to their beta-anomers
associated with microtubules and essential; regulator of
microtubule stability
Protein with weak similarity to D. melanogaster serendipity
protein and X. laevis basis fibroblast growth factor
None
Chitin synthase II, requires activation from zymogenic form in
order to catalyze the transfer of N-acetylglucosamine (GlcNAc)
to chitin; required for the synthesis of chitin in the primary
septum during cytokinesis
YBR295W
PCA1
YBR287W
ZSP1
YJR091C
JSN1
YPR002W
PDH1
YBR255W
None
YBL033C
RIB1
YBL017C
PEP1
P-type metal-transporting ATPase with a role in copper and iron
homeostasis; R970G-substitution in the C-terminal region
confers cadmium resistance
None
Member of the Puf family of RNA-binding proteins, interacts
with mRNAs encoding membrane-associated proteins;
overexpression suppresses a tub2-150 mutation and causes
increased sensitivity to benomyl in wild-type cells
Mitochondrial protein that participates in respiration, induced by
diauxic shift; homologous to E. coli PrpD, may take part in the
conversion of 2-methylcitrate to 2-methylisocitrate
GTP cyclohydrolase II; catalyzes the first step of the riboflavin
Type I transmembrane sorting receptor for multiple vacuolar
hydrolases; cycles between the late-Golgi and prevacuolar
endosome-like compartments
(35) MODULE 40
YGL180W
ATG1
YOR224C
RPB8
YGR097W
ASK10
YCL055W
KAR4
YJL089W
SIP4
YCL055W
KAR4
YJR122W
CAF17
I, II, and III
Transcription factor required for induction of KAR3 and CIK1
during mating, also required during meiosis; exists in two forms,
a slower-migrating form more abundant during vegetative
growth and a faster-migrating form induced by pheromone
transcription
proteins
Module genes
YBR010W
HHT1
YNL024C
None
phosphorylation
YBR177C
EHT1
YGL225W
VRG4
YDR225W
HTA1
YER070W
RNR1
YLR112W
None
YPL127C
HHO1
YBR009C
HHF1
YML027W
YOX1
YDR222W
YMR199W
YBR070C
None
CLN1
None
YDR224C
HTB1
YIL016W
SNL1
YBL003C
HTA2
YML052W
SUR7
YOL007C
None
YCR034W
FEN1
YBL002W
HTB2
Possible serine hydrolase, may be involved in lipid metabolism,
null mutant slightly temperature sensitive at 37C
May regulate Golgi function and glycosylation in Golgi; Golgi
GDP-mannose transporter
Ribonucleotide-diphosphate reductase (RNR), large subunit; the
Histone H1, a linker histone required for nucleosome packaging
at restricted sites; suppresses DNA repair involving homologous
recombination; not required for telomeric silencing, basal
transcriptional repression, or efficient sporulation
Homeodomain-containing transcriptional repressor, binds to
Mcm1p and to early cell cycle boxes (ECBs) in the promoters of
cell cycle-regulated genes expressed in M/G1 phase; expression
is cell cycle-regulated; potential Cdc28p substrate
methylation
Integral membrane protein containing a Bag domain; suppressor
of nup116-C lethal
Multicopy suppressor of rvs167 mutation; putative integral
membrane protein
Fatty acid elongase, involved in sphingolipid biosynthesis; acts
on fatty acids of up to 24 carbons in length; mutations have
regulatory effects on 1,3-beta-glucan synthase, vacuolar
ATPase, and the secretory pathway
methylation
YMR292W
GOT1
YOR045W
TOM6
YOR067C
ALG8
YMR003W
YOR101W
None
RAS1
YNL031C
HHT2
YHR153C
YPL144W
SPO16
None
YPR052C
NHP6A
YMR318C
ADH6
YNL030W
HHF2
Golgi Transport; membrane protein
involved in supporting the cooperativity between receptors and
the general insertion pore and facilitating the release of
preproteins from import components; outer mitochondrial
membrane protein, component of the mitochondiral protein
translocation complex, associates with TOM40
adds glucose to the dolichol-linked oligosaccharide precursor
prior to transfer to protein; glycosyl transferase
phosphorylation
Protein of unknown function, required for spore formation
NADPH-dependent alcohol dehydrogenase
(36) MODULE 41
Genotype regulators
YAR019W-A PAU7(0,2) YAR023C UIP3(9,133) YAR028W
YAR029W YAR030C PRM9(60,6) MST28(5,7) YAR035C-A
YAT1(2,63) SWH1(10,11) YAR044W
M1_184243_187272
Module genes
YAR027W
UIP3
YAR028W
(37) MODULE 42
Genotype regulators
None
Putative integral membrane protein of unknown function;
interacts with Ulp1p at the nuclear periphery; member of
DUP240 gene family
HAT1(2,2) SNF8(0,2) ULA1(2,0) LSP1(0,0) AEP3(2,0)
NCR1(0,3) TFC8(1,3) CHL1(2,1) YPL009C RET3(1,2)
TAF3(1,2) RRP12(5,1) MRPS16(0,1) YPL014W HST2(1,2)
CIT3(0,23) YPR002C-A PDH1(0,0) YPR003C YPR004C
M16_533282_555416
Module genes
YPL002C
SNF8
YPR006C
ICL2
appears to be functionally related to SNF7; involved in glucose
derepression
2-methylisocitrate lyase of the mitochondrial matrix, functions
in the methylcitrate cycle to catalyze the conversion of 2methylisocitrate to succinate and pyruvate; ICL2 transcription is
repressed by glucose and induced by ethanol
(38) MODULE 43
YDR043C
NRG1
YGR014W
MSB2
Protein that functions as an osmosensor in parallel to the Sho1pmediated pathway, multicopy suppressor of a temperaturesensitive mutation in CDC24, potential Cdc28p substrate
Genotype regulators
ICS2(1,5) AMN1(3,17) YBR159W CDC28(0,5) CSH1(0,3)
TOS1(2,3) YSY6(1,3) DEM1(6,5) ARL1(0,5) UBS1(0,5)
TYR1(7,5) POP7(1,4) PEX32(4,4) SSE2(4,7) NPL4(2,1)
SEC66(0,1)
M2_562409_570229
Module genes
YNR067C
DSE4
YBR132C
AGP2
YJL078C
PRY3
YOR264W
DSE3
YER124C
DSE1
YGR041W
BUD9
YGL028C
SCW11
YMR285C
NGL2
YKL132C
YOR263C
YNL078W
RMA1
None
NIS1
YBR158W
AMN1
YHR143W
DSE2
YPR106W
ISR1
YNL066W
SUN4
YNL327W
EGT2
Daughter cell-specific secreted protein with similarity to
glucanases, degrades cell wall from the daughter side causing
daughter to separate from mother
Plasma membrane carnitine transporter, expression is downregulated by osmotic stress; also functions as a low-affinity
amino acid permease
Daughter cell-specific protein, may help establish daughter fate
Daughter cell-specific protein, may participate in pathways
regulating cell wall metabolism; deletion affects cell separation
after division and sensitivity to drugs targeted against the cell
wall
unipolar budding pattern instead of the wild-type bipolar pattern,
and bud at the distal pole
Cell wall protein with similarity to glucanases; may play a role
in conjugation during mating based on its regulation by Ste12p
RNase required for correct 3'-end formation of 5.8S rRNA at
site E; has similarity to Ngl1p and Ngl3p and to drosophila
Angelgene
probable folyl-polyglutamate synthetase
None
Involved in daughter cell separation and Chromosome STability;
Chromosome STability
Daughter cell-specific secreted protein with similarity to
glucanases, degrades cell wall from the daughter side causing
daughter to separate from mother; expression is repressed by
cAMP
Predicted protein kinase, overexpression causes sensitivity to
staurosporine, which is a potent inhibitor of protein kinase C
Protein involved in the aging process; related to glucanases
Glycosylphosphatidylinositol (GPI)-anchored cell wall
endoglucanase required for proper cell separation after
cytokinesis, expression is activated by Swi5p and tightly
regulated in a cell cycle-dependent manner
(39) MODULE 44
YGL208W
SIP2
YOR337W
TEA1
YOR101W
YPL230W
RAS1
None
YKL109W
HAP4
YFR009W
GCN20
YIL033C
BCY1
Module genes
YOL092W
None
YMR038C
CCS1
YDR046C
BAP3
YER086W
ILV1
YGR061C
ADE6
YHR020W
None
YDR037W
KRS1
YNR046W
None
YPR033C
HTS1
YOL046C
None
YGR124W
ASN2
Member of a family of proteins, including Sip1p and Gal83p,
that interact with Snf1p and Snf4p and are involved in the
response to glucose starvation; component of Snf1 protein
complex involved in response to glucose starvation
uncharged tRNA
Copper chaperone for superoxide dismutase Sod1p, involved in
oxidative stress protection; Met-X-Cys-X2-Cys motif within the
N-terminal portion is involved in insertion of copper into Sod1p
under conditions of copper deprivation
Amino acid permease involved in the uptake of cysteine,
leucine, isoleucine and valine
Threonine deaminase, catalyzes the first step in isoleucine
biosynthesis; expression is under general amino acid control;
ILV1 locus exhibits highly positioned nucleosomes whose
organization is independent of known ILV1 regulation
Formylglycinamidine-ribonucleotide (FGAM)-synthetase,
catalyzes a step in the 'de novo' purine nucleotide biosynthetic
pathway
Lysyl-tRNA synthetase; also identified as a negative regulator of
general control of amino acid biosynthesis
Cytoplasmic and mitochondrial histidine tRNA synthetase;
encoded by a single nuclear gene that specifies two messages;
efficient mitochondrial localization requires both a presequence
and an amino-terminal sequence
Asparagine synthetase, isozyme of Asn1p; catalyzes the
synthesis of L-asparagine from L-aspartate in the asparagine
YHR025W
THR1
YGL234W
ADE5,7
YHR047C
AAP1'
YHR063C
PAN5
YCR053W
THR4
YLR331C
JIP3
YNL095C
None
YHR014W
SPO13
YLR359W
ADE13
YGL071W
RCS1
YGL039W
YDR341C
None
None
YOR323C
PRO2
YOR262W
None
YPL160W
CDC60
YKR099W
BAS1
YKL072W
(40) MODULE 46
STB6
YGR070W
ROM1
YGL248W
PDE1
YCR091W
KIN82
YOL113W
SKM1
YGR200C
ELP2
homoserine kinase
Bifunctional enzyme of the 'de novo' purine nucleotide
biosynthetic pathway, contains aminoimidazole ribotide
synthetase and glycinamide ribotide synthetase activities
Arginine/alanine aminopeptidase, overproduction stimulates
glycogen accumulation
2-dehydropantoate 2-reductase, part of the pantothenic acid
pathway, structurally homologous to E. coli panE
threonine synthase
ORF overlaps the verified gene MID2
Meiosis-specific protein of unknown function, involved in
maintaining sister chromatid cohesion during meiosis I as well
as promoting proper attachment of kinetochores to the spindle
during meiosis I and meiosis II
Adenylosuccinate lyase, catalyzes two steps in the 'de novo'
purine nucleotide biosynthetic pathway
Transcription factor that binds the consensus site
PyPuCACCCPu, involved in iron homeostasis and cell size
regulation; activates the expression of target genes in response
to low-iron conditions
Gamma-glutamyl phosphate reductase, catalyzes the second step
in proline biosynthesis
Cytosolic leucyl tRNA synthetase, ligates leucine to the
appropriate tRNA
binds Sin3p in two-hybrid assay; involved in transcription
a GEP
Low-affinity cyclic AMP phosphodiesterase, controls glucose
and intracellular acidification-induced cAMP signaling, target of
the cAMP-protein kinase A (PKA) pathway; glucose induces
transcription and inhibits translation
kinase C subfamily
Serine/threonine protein kinase with similarity to Ste20p and
Cla4p
YJL098W
SAP185
YIL101C
XBP1
Module genes
YDR058C
YOR228C
TGL2
None
YEL060C
PRB1
YKR067W
GPT2
YBR269C
FMP21
YLR164W
None
YMR020W
FMS1
YCR068W
ATG15
YBL078C
ATG8
YMR279C
YER039C
YOR152C
None
HVG1
None
YML118W
NGL3
YNL223W
ATG4
YJL057C
None
YLR080W
EMP46
YHR138C
YDR018C
YML042W
None
None
CAT2
Triglyceride Lipase
Vacuolar proteinase B (yscB), a serine protease of the subtilisin
family; involved in protein degradation in the vacuole and
required for full protein degradation during sporulation
Glycerol-3-phosphate acyltransferase located in both lipid
particles and the ER; involved in the stepwise acylation of
glycerol-3-phosphate and dihydroxyacetone, which are
intermediate steps in lipid biosynthesis
mitochondria
Polyamine oxidase, converts spermine to spermidine, which is
required for the essential hypusination modification of
translation factor eIF-5A; also involved in pantothenic acid
biosynthesis
Lipase, required for intravacuolar lysis of autophagic bodies;
located in the endoplasmic reticulum membrane and targeted to
intravacuolar vesicles during autophagy via the multivesicular
body (MVB) pathway
Forms a protein complex with Aut2p to mediate attachment of
autophagosomes to microtubules. Defective in maturation of the
vacuolar protein, aminopeptidase I; Aut7p has homology to
LC3, a microtubule-associated protein from rat.
Protein of unknown function, has homology to Vrg4p
DNase/RNase (putative); CCR4 C-terminal homolog; displays
homology to drosophila Angel gene; homolog to ngl1 and ngl2
Anchor protein involved in autophagy and required for
sporulation; interacts with Tub1p and Tub2p and forms a
complex with Aut7p; mediates attachment of autophagosomes to
microtubules
Integral membrane component of endoplasmic reticulumderived COPII-coated vesicles, which function in ER to Golgi
transport
Carnitine O-acetyltransferase, peroxisomal and mitochondrial
YGR045C
YJL141C
YPL247C
None
YAK1
None
YDR358W
GGA1
YDL072C
YET3
YBR241C
None
YDR059C
UBC5
YBL049W
YIL077C
YJL132W
MOH1
None
None
YAL028W
FRT2
YPL166W
YMR262W
None
None
YOR137C
SIA1
YER079W
YDL169C
YGR066C
YFL042C
YKL121W
None
UGX2
None
None
None
YGR281W
YOR1
YDR043C
NRG1
YIR018W
YAP5
YNL116W
DMA2
YJL070C
None
YAL054C
ACS1
YPL222W
FMP40
YOR121C
YIL017C
None
VID28
Golgi-localized protein with homology to gamma-adaptin,
interacts with and regulates Arf1p and Arf2p in a GTPdependent manner in order to facilitate traffic through the late
Golgi
human BAP31 protein
Ubiquitin-conjugating enzyme that mediates selective
degradation of short-lived and abnormal proteins, central
component of the cellular stress response; expression is heat
inducible
Protein of unknown function, has homology to kinase Snf7p
Tail-anchored endoplasmic reticulum membrane protein,
interacts with homolog Frt1p but is not a substrate of calcineurin
(unlike Frt1p), promotes growth in conditions of high Na+,
alkaline pH, or cell wall stress; potential Cdc28p substrate
Suppressor of eIF5A; High-copy suppressor of temperaturesensitive tif51A-1
Plasma membrane transporter of the ATP-binding cassette
(ABC) family, mediates export of many different organic anions
including oligomycin
Protein involved in regulating spindle position and orientation,
functionally redundant with Dma1p; homolog of S. pombe
Dma1 and H. sapiens Chfr
one of 2 acetyl-coA synthetases in yeast; inducible acetylcoenzyme A synthetase
mitochondria.
Vacuole import and degradation
YFR017C
None
YBR001C
NTH2
YAL034C
FUN19
YPL018W
CTF19
YKL188C
PXA2
YMR291W
None
YMR195W
ICY1
YER035W
EDC2
YHL027W
RIM101
YBR046C
ZTA1
YJL079C
PRY1
YKL103C
LAP4
YPL006W
NCR1
YLL040C
VPS13
YOR040W
GLO4
YOR120W
GCY1
YPR155C
NCA2
YJL163C
YGR067C
YMR251W
None
None
None
YDR525W-A
SNA2
Neutral trehalase, degrades trehalose; required for
thermotolerance and may mediate resistance to other cellular
stresses
Outer kinetochore protein, required for accurate mitotic
chromosome segregation; forms a complex with Mcm21p and
Okp1p that binds to centromeres via the CBF3 complex
Homolog of the human adrenoleukodystrophy transporter; forms
a heterodimer with Pxa1p of two half ATP-binding cassette
transporters in the peroxisome membrane; peroxisomal ABC
transporter 2
Protein that interacts with the cytoskeleton and is involved in
chromatin organization and nuclear transport, interacts
genetically with TCP1 and ICY2, required for viability in rich
media of cells lacking mitochondrial DNA
RNA-binding protein, activates mRNA decapping directly by
binding to the mRNA substrate and enhancing the activity of the
decapping proteins Dcp1p and Dcp2p
Transcriptional activator required for entry into meiosis, has
similarity to the Aspergillus Phenotype-response regulator PacC
and the Yarrowia proteinase YlRim1010p; Meiotic regulatory
protein; Cys-His zinc fingers
Zeta-crystallin homolog, found in the cytoplasm and nucleus;
has similarity to E. coli quinone oxidoreductase and to human
zeta-crystallin, which has quinone oxidoreductase activity
Vacuolar aminopeptidase, often used as a marker protein in
studies of autophagy and cytosol to vacuole targeting (CTV)
pathway
A transmembrane glycoprotein that is homologous to human
Niemann-Pick Type C (NPC) gene; involved in sphingolipid
metabolism; predicted transmembrane protein
homologous to human COH1; component of peripheral vacuolar
membrane protein complex
Mitochondrial glyoxalase II, catalyzes the hydrolysis of S-Dlactoylglutathione into glutathione and D-lactate
Putative NADP(+) coupled glycerol dehydrogenase, proposed to
be involved in an alternative pathway for glycerol catabolism
Regulates proper expression of subunits 6 (Atp6p) and 8
(Atp8p) of the Fo-F1 ATP synthase; Regulates expression of
mitochondrial ATP synthase
Protein of unknown function, has similarity to Pmp3p, which is
involved in cation transport; green fluorescent protein (GFP)fusion protein localizes to the cytoplasm in a punctate pattern
YPL177C
CUP9
YLR375W
STP3
YDR055W
PST1
YJR008W
YIL042C
YOR347C
None
None
PYK2
YMR261C
TPS3
YMR253C
YPL165C
None
SET6
YHR171W
ATG7
YHL021C
FMP12
YDL085W
YDL199C
YLR312C
YPR003C
YOR186W
NDE2
None
None
None
None
YNL242W
ATG2
YKR058W
GLG1
YJL210W
PEX2
YMR053C
STB2
YOR215C
None
YFR047C
BNA6
YBR214W
SDS24
YBR280C
YPL017C
None
None
YKL129C
MYO3
YKL065C
YET1
Homeodomain-containing transcriptional repressor of PTR2,
which encodes a major peptide transporter; imported peptides
activate ubiquitin-dependent proteolysis, resulting in
degradation of Cup9p and de-repression of PTR2 transcription
Protein involved in pre-tRNA splicing and in uptake of
branched-chain amino acids
Cell wall protein that contains a putative GPI-attachment site;
secreted by regenerating protoplasts; up-regulated by activation
of the cell integrity pathway, as mediated by Rlm1p; upregulated
by cell wall damage via disruption of FKS1
Pyruvate kinase, glucose-repressed isoform; pyruvate kinase
115 kD regulatory subunit of trehalose-6-phosphate
synthase/phosphatase complex
None
autophagy; similar to ubiquitin-activating enzymes, involved in
autophagy
mitochondria
None
Defective in autophagy; required for sporulation; Required for
sporulation.
Self-glucosylating initiator of glycogen synthesis, also
glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian
glycogenin
C3HC4 zinc-binding integral peroxisomal membrane protein;
Pex2p, Pex10p, and Pex12p together make up the RING finger
complex of the peroxisomal import machinery
Protein that binds Sin3p in a two-hybrid assay and is part of a
large protein complex with Sin3p and Stb1p
Quinolinate phosphoribosyl transferase, required for
biosynthesis of nicotinic acid from tryptophan via kynurenine
pathway
Nuclear protein with similarity to S. pombe Sds23, suppresses
dis2 mutations
One of two class-I myosins; localizes to actin cortical patches;
deletion of MYO3 has little affect on growth, but myo3 myo5
double deletion causes severe defects in growth and actin
cytoskeletion organization; myosin I
YGL121C
GPG1
YMR304W
UBP15
YDR530C
APA2
YNL011C
YFR043C
None
None
YJL116C
NCA3
YLR356W
None
YDR204W
COQ4
YCL038C
ATG22
YER037W
PHM8
YOR134W
BAG7
YBR006W
UGA2
YPR127W
None
YMR322C
SNO4
YNR002C
FUN34
human BAP31 protein
Gpa2p
Ubiquitin-specific protease that may play a role in ubiquitin
precursor processing
Diadenosine 5',5''-P1,P4-tetraphosphate phosphorylase II (AP4A
phosphorylase), involved in catabolism of bis(5'-nucleosidyl)
tetraphosphates; has similarity to Apa1p
With NCA2, regulates proper expression of subunits 6 (Atp6p)
and 8 (Atp8p ) of the Fo-F1 ATP synthase; involved in
regulating expression of F0F1 ATPase subunits
Protein with a role in ubiquinone (Coenzyme Q) biosynthesis,
possibly functioning in stabilization of Coq7p; located on the
matrix face of the mitochondrial inner membrane
Autophagy gene essential for breakdown of autophagic vesicles
in the vacuole
Protein of unknown function, expression is induced by low
phosphate levels and by inactivation of Pho85p
Rho GTPase activating protein (RhoGAP), stimulates the
intrinsic GTPase activity of Rho1p, which plays a role in actin
cytoskeleton organization and control of cell wall synthesis;
structurally and functionally related to Sac7p
involved in utilization of GABA as a nitrogen source; succinate
semialdehyde dehydrogenase
coli Hsp31 and S. cerevisiae Hsp31p, Hsp32p, and Hsp33p;
member of the DJ-1/ThiJ/PfpI superfamily; may have a role in
pyridoxine metabolism
Putative transmembrane protein, involved in ammonia
production; member of the TC 9.B.33 YaaH family; homolog of
Ady2p and Y. lipolytica Gpr1p
(41) MODULE 48
YIR017C
MET28
YOR178C
GAC1
YJL164C
TPK1
YJL157C
FAR1
YJL103C
None
Cyclin-dependent kinase inhibitor that mediates cell cycle arrest
in response to pheromone; also forms a complex with Cdc24p,
Ste4p, and Ste18p that may specify the direction of polarized
growth during mating; potential Cdc28p substrate
YER054C
GIP2
YER054C
GIP2
Pig1p, and Pig2p
Pig1p, and Pig2p
Module genes
YDR402C
DIT2
YPL265W
DIP5
YER091C
MET6
YJR146W
None
YKL001C
MET14
YGL153W
PEX14
YDL114W
None
YOL158C
ENB1
YHR046C
INM1
YPR048W
TAH18
YNR034W
SOL1
YJR010W
MET3
YLR302C
None
YDR384C
ATO3
YIL168W
YEL072W
None
RMD6
Sporulation-specific enzyme required for spore wall maturation,
involved in the production of a soluble LL-dityrosine-containing
precursor of the spore wall, homologous to cytochrome P-450s
Dicarboxylic amino acid permease, mediates high-affinity and
high-capacity transport of L-glutamate and L-aspartate; also a
transporter for Gln, Asn, Ser, Ala, and Gly
Cobalamin-independent methionine synthase, involved in amino
acid biosynthesis; also called N5-methyltetrahydrofolate
homocysteine methyltransferase or 5methyltetrahydropteroyltriglutamate homocysteine
methyltransferase
Adenylylsulfate kinase, required for sulfate assimilation and
involved in methionine metabolism
Peroxisomal peripheral membrane protein (peroxin) involved in
import of peroxisomal matrix proteins; component of
peroxisomal import machinery
Endosomal ferric enterobactin transporter, expressed under
conditions of iron deprivation; member of the major facilitator
superfamily; expression is regulated by Rcs1p and affected by
chloroquine treatment
Inositol monophosphatase, involved in biosynthesis of inositol
and in phosphoinositide second messenger signalling; INM1
expression increases in the presence of inositol and decreases
upon exposure to antibipolar drugs lithium and valproate
Protein with a potential role in DNA replication; displays
synthetic lethal genetic interaction with the pol3-13 allele of
POL3, which encodes DNA polymerase delta
Multicopy Suppressor Of los1; shows similarity to glucose-6phosphate dehydrogenase non-catalytic domains; homologous to
Sol2p and Sol3p
ATP sulfurylase, catalyzes the primary step of intracellular
sulfate activation, essential for assimilatory reduction of sulfate
to sulfide, involved in methionine metabolism
Plasma membrane protein, regulation pattern suggests a possible
role in export of ammonia from the cell; member of the TC
9.B.33 YaaH family of putative transporters
Protein required for sporulation
YLR355C
ILV5
YMR058W
FET3
YNL318C
HXT14
YIL105C
SLM1
YEL008W
None
YPL130W
SPO19
YPL080C
None
YEL065W
SIT1
YJL127C
SPT10
YIL053W
RHR2
YIL163C
YNL276C
None
None
YOL059W
GPD2
YLR307W
CDA1
YDL059C
RAD59
YJL212C
OPT1
YPL058C
PDR12
Acetohydroxyacid reductoisomerase, mitochondrial protein
involved in branched-chain amino acid biosynthesis, also
required for maintenance of wild-type mitochondrial DNA
Ferro-O2-oxidoreductase required for high-affinity iron uptake
and involved in mediating resistance to copper ion toxicity,
belongs to class of integral membrane multicopper oxidases
Protein of unknown function; mutation is synthetically lethal
with an mss4 mutation
Meiosis-specific protein of unknown function, involved in
completion of nuclear divisions; identified as a weak high-copy
suppressor of the spo1-1 ts mutation; putative GPI-dependent
cell-wall protein
Ferrioxamine B transporter, member of the ARN family of
transporters that specifically recognize siderophore-iron
chelates; transcription is induced during iron deprivation and
diauxic shift; potentially phosphorylated by Cdc28p
Putative histone acetylase, required for transcriptional regulation
at core promoters, functions at or near the TATA box
Constitutively expressed isoform of DL-glycerol-3-phosphatase;
involved in glycerol biosynthesis, induced in response to both
anaerobic and, along with the Hor2p/Gpp2p isoform, osmotic
stress
Involved in glycerol production via conversion of glyerol-3phosphate and NAD+ to glycerol phosphate and NADH;
Glycerol-3-phosphate dehydrogenase (NAD+)
Required for proper formation of the ascospore wall; Chitin
Deacetylase
Protein involved in the repair of double-strand breaks in DNA
during vegetative growth via recombination and single-strand
annealing; anneals complementary single-stranded DNA;
homologous to Rad52p
Plasma membrane transporter that transports tetra- and
pentapeptides and glutathione; member of the OPT family
Plasma membrane weak-acid-inducible ATP-binding cassette
(ABC) transporter, required for weak organic acid resistance,
strongly induced by sorbate and benzoate, regulated by War1p,
mutants exhibit sorbate hypersensitivity
(42) MODULE 49
YOL113W
SKM1
YIL147C
SLN1
Cla4p
regulators
Genotype regulators
YMR310C GLC8(0,3) ELP6(1,3) TGL3(1,5) PRE5(0,5)
YMR315W YMR315W-A YMR316C-A YMR316C-B
DIA1(1,4) YMR317W ADH6(0,8) FET4(1,8) YMR320W
YMR321C SNO4(1,20) ERR3 YMR324C YMR325W
YMR326C
M13_905780_922268
Module genes
YPL273W
SAM4
YPL279C
None
YPL274W
SAM3
YOR389W
YPL277C
YOR390W
YMR321C
YPL278C
(43) MODULE 50
None
None
None
None
None
YBR158W
AMN1
YOR047C
STD1
YGR108W
YBL066C
YPR013C
Module genes
CLB1
SEF1
None
YAL020C
ATS1
YGR203W
YLR414C
None
None
YCR073W-A
SOL2
YNL241C
YPL067C
YBR148W
YLR042C
ZWF1
None
YSW1
None
YLR099C
ICT1
S-adenosylmethionine-homocysteine methyltransferase,
functions along with Mht1p in the conversion of Sadenosylmethionine (AdoMet) to methionine to control the
methionine/AdoMet ratio
High-affinity S-adenosylmethionine permease, required for
utilization of S-adenosylmethionine as a sulfur source; has
similarity to S-methylmethionine permease Mmp1p
Protein that interacts with the Snf1p protein kinase and Spt15p
in two-hybrid and in in vitro binding studies
Protein with a potential role in regulatory interactions between
microtubules and the cell cycle, as suggested by genetic and
physical interactions with Nap1p and genetic interactions with
TUB1
multicopy suppressor of los1-1; shows similarity to glucose-6phosphate dehydrogenase non-catalytic domains; homologous to
Sol1p and Sol3p
Glucose-6-phosphate dehydrogenase
Protein expressed specifically in spores
Protein of unknown function, null mutation leads to an increase
in sensitivity to Calcofluor white; expression of the gene is
induced in the presence of isooctane
YOR084W
YNL300W
None
None
YNL322C
KRE1
YCL044C
YBR150C
YIL153W
None
TBS1
RRD1
YOL110W
SHR5
YER004W
FMP52
YDR156W
RPA14
YGR014W
MSB2
YLR337C
VRP1
YER018C
SPC25
YFR051C
RET2
YFL031W
HAC1
Cell wall glycoprotein involved in beta-glucan assembly; serves
as a K1 killer toxin membrane receptor
Resistant to Rapamycin Deletion
Subunit of a palmitoyltransferase, composed of Shr5p and
Erf2p, that adds a palmitoyl lipid moiety to Ras2p through a
thioester linkage; palmitoylation is required for Ras2p
localization to the plasma membrane
mitochondria
RNA polymerase I subunit A14
Involved in cytoskeletal organization and cellular growth;
Proline-rich protein verprolin
Spindle pole body (SPB) component, localizes to the nuclear
side of spindle pole; interacts with Nuf2p, Ndc80p, and Spc24p
at the kinetochore; has a putative role in spindle checkpoint
control and centromere clustering at spindle pole
Delta subunit of the coatomer complex (COPI), which coats
Golgi-derived transport vesicles; involved in retrograde
transport between Golgi and ER
synthesis
(44) MODULE 51
YJL098W
SAP185
YJL098W
SAP185
YJL098W
SAP185
YHR030C
YJL164C
SLT2
TPK1
YCR091W
KIN82
YJL164C
TPK1
kinase C subfamily
Module genes
YMR185W
YOR340C
None
RPA43
YOR195W
SLK19
YNL075W
IMP4
YGR245C
SDA1
YKL021C
MAK11
YBR155W
CNS1
YAL019W
FUN30
YMR310C
None
YPL012W
RRP12
YLR068W
FYV7
YHR052W
CIC1
YMR093W
UTP15
YPL093W
NOG1
YHR197W
RIX1
YDR165W
TRM82
YOR144C
ELG1
YOR048C
RAT1
YKR024C
DBP7
YDL150W
RPC53
YOL041C
NOP12
Kinetochore-associated protein required for normal segregation
of chromosomes in meiosis and mitosis; component of the
FEAR regulatory network, which promotes Cdc14p release from
the nucleolus during anaphase; potential Cdc28p substrate
Component of the SSU processome, which is required for pre18S rRNA processing; interacts with Mpp10p; member of a
superfamily of proteins that contain a sigma(70)-like motif and
associate with RNAs
Severe Depolymerization of Actin
Protein essential for cell growth and replication of M dsRNA
virus; contains four beta-transducin repeats
cyclophilin seven suppressor; component of Hsp90p chaperone
machinery
Protein whose overexpression affects chromosome stability,
potential Cdc28p substrate; homolog of Snf2p
Protein required for normal pre-rRNA Processing; member of a
group of seven genes whose expression is repressed during
growth on glucose before and during the diauxic shift
exposure to K1 killer toxin; involved in processing the 35S
rRNA primary transcript to generate the 20S and 27SA2 prerRNA transcripts
Core interacting component 1; ribosome biogenesis protein
Putative GTPase that associates with free 60S ribosomal
subunits in the nucleolus and is required for 60S ribosomal
subunit biogenesis; member of the ODN family of nucleolar Gproteins
RIbosome eXport; Protein required for cell viability
Subunit of a tRNA methyltransferase complex composed of
Trm8p and Trm82p that catalyzes 7-methylguanosine
modification of tRNA
Protein required for S phase progression and telomere
homeostasis, forms an alternative replication factor C complex
important for DNA replication and genome integrity; mutants
are sensitive to DNA damage
RNA trafficking protein; transcription activator
Putative ATP-dependent RNA helicase of the DEAD-box family
involved in ribosomal biogenesis
RNA polymerase III subunit C53
Nucleolar protein, required for pre-25S rRNA processing;
contains an RNA recognition motif (RRM) and has similarity to
Nop13p, Nsr1p, and putative orthologs in Drosophila and S.
pombe
YNL207W
RIO2
YGR103W
NOP7
YOL144W
NOP8
YKL082C
RRP14
YLR449W
FPR4
YHR169W
DBP8
YJR003C
None
YCL059C
KRR1
YFL034C-A
RPL22B
YDL148C
NOP14
YOR091W
None
YJL109C
UTP10
YNL292W
PUS4
YGR228W
YJL148W
None
RPA34
YMR239C
RNT1
YHR085W
IPI1
YDR496C
YKR081C
PUF6
RPF2
YAL025C
MAK16
YLR074C
BUD20
YCR016W
None
YNR003C
RPC34
YHR081W
LRP1
Nucleolar protein involved in rRNA processing and 60S
ribosomal subunit biogenesis; constituent of several different
pre-ribosomal particles
Nucleolar protein required for 60S ribosomal subunit biogenesis
Required for normal pre-rRNA Processing; Protein required for
cell viability
Nuclear protein, putative peptidyl-prolyl cis-trans isomerase
(PPIase) with similarity to Fpr3p; overproduction suppresses the
growth defect resulting from the absence of E3 ubiquitin-protein
ligase Tom1p
involved in biogenesis of the 40S ribosomal subunit
Essential nucleolar protein required for the synthesis of 18S
rRNA and for the assembly of 40S ribosomal subunit
Protein component of the large (60S) ribosomal subunit, has
similarity to Rpl22Ap and to rat L22 ribosomal protein
Nucleolar protein, forms a complex with Noc4p that mediates
maturation and nuclear export of 40S ribosomal subunits; also
present in the small subunit processome complex, which is
required for processing of pre-18S rRNA
catalyzes formation of Psi55 (modified uridine) in mitochondrial
and cytoplasmic tRNAs; Pseudouridine synthase
RNA polymerase I subunit A34.5
RNAase III; cleaves a stem-loop structure at the 3' end of U2
snRNA to ensure formation of the correct U2 3' end
Protein of unknown function, essential for viability, may be
involved in rRNA processing
None
Essential nuclear protein required for normal concentration of
free 60S ribosomal subunits; required for maintenance of M1
satellite double-stranded RNA of the L-A virus
RNA polymerase III subunit C34; interacts with TFIIIB70 and is
a key determinant in pol III recruitment by the preinitiation
complex
Protein involved in homologous recombination and in nonhomologous DNA end joining; homolog of mammalian C1D,
which is a nuclear matrix protein involved in regulation of DNA
repair and recombination
YJR002W
MPP10
YIL020C
HIS6
YDL036C
None
YIL019W
FAF1
YLR222C
UTP13
YGR140W
CBF2
YKL014C
URB1
YLR287C
None
YDR021W
FAL1
YER006W
NUG1
YCL054W
SPB1
YOR145C
PNO1
YDR399W
HPT1
YKR056W
TRM2
YLR106C
MDN1
YLR129W
DIP2
YMR131C
RRB1
YKL009W
MRT4
YDR299W
BFR2
YOR252W
None
Component of the SSU processome, which is required for pre18S rRNA processing, interacts with and controls the stability of
Imp3p and Imp4p, essential for viability
Phosphoribosyl-5-amino-1-phosphoribosyl-4imidazolecarboxiamide isomerase, catalyzes the fourth step in
histidine biosynthesis; mutations cause histidine auxotrophy and
sensitivity to Cu, Co, and Ni salts
Protein required for pre-rRNA processing and 40S ribosomal
subunit assembly
Essential kinetochore protein, component of the CBF3
multisubunit complex that binds to the CDEIII region of the
centromere; Cbf2p also binds to the CDEII region possibly
forming a different multimeric complex, ubiquitinated in vivo
Nucleolar protein required for the normal accumulation of 25S
and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal
particle; proposed to be involved in the biogenesis of the 60S
ribosomal subunit
Nucleolar protein required for maturation of 18S rRNA, member
of the eIF4A subfamily of DEAD-box ATP-dependent RNA
helicases
GTPase that associates with nuclear 60S pre-ribosomes, required
for export of 60S ribosomal subuits from the nucleus
Suppressor of PaB1 mutant; encodes a S-adenosylmethioninedependent methyltransferase; involved in 60S ribosomal subunit
biogenesis and rRNA processing; Putative methyltransferase
Partner of Nob1; Protein required for cell viability
enzyme involved in de novo purine biosynthesis; hypoxanthine
guanine phosphoribosyltransferase
tRNA methyltransferase, 5-methylates the uridine residue at
position 54 of tRNAs and may also have a role in tRNA
stabilization or maturation; previously thought to be an endoexonuclease
Midasin, pseudo-hexameric assembly of AAA protomers
associated with a C-terminal MIDAS-containing M-domain,
associated with 60S pre-ribosomes (large subunit precursor) and
their export from the nucleus
Nucleolar protein, specifically associated with the U3 snoRNA,
part of the large ribonucleoprotein complex known as the small
subunit (SSU) processome, required for 18S rRNA biogenesis,
part of the active pre-rRNA processing complex
RiboSome Assembly 2
Protein involved in mRNA turnover and ribosome assembly,
localizes to the nucleolus
Essential protein possibly involved in secretion; multicopy
suppressor of sensitivity to Brefeldin A
YOL022C
None
YNL166C
BNI5
YNL182C
IPI3
YNL132W
KRE33
YKR060W
UTP30
YOL109W
ZEO1
YGR173W
RBG2
YPL126W
NAN1
YKL078W
DHR2
YDR184C
ATC1
YER127W
LCP5
YDL031W
DBP10
YDL153C
SAS10
YNL112W
DBP2
YFL002C
SPB4
YLR009W
RLP24
YGR187C
HGH1
YGR145W
ENP2
YHR154W
RTT107
YHR170W
NMD3
YDR324C
UTP4
YMR179W
SPT21
Protein involved in organization of septins at the mother-bud
neck, may interact directly with the Cdc11p septin, localizes to
bud neck in a septin-dependent manner
Protein required for cell viability; computational analysis of
large-scale protein-protein interaction data suggests a possible
role in assembly of the ribosomal large subunit
Essential protein of unknown function; heterozygous mutant
shows haploinsufficiency in K1 killer toxin resistance
Possible U3 snoRNP protein involved in maturation of pre-18S
rRNA, based on computational analysis of large-scale proteinprotein interaction data
Peripheral membrane protein of the plasma membrane that
interacts with Mid2p; regulates the cell integrity pathway
mediated by Pkc1p and Slt2p
Protein with similarity to mammalian developmentally regulated
GTP-binding protein
part of small (ribosomal) subunit (SSU) processosome (contains
U3 snoRNA); Net1-Associated Nucleolar protein 1; Net1Associated Nucleolar protein 1
Predominantly nucleolar DEAH-box RNA helicase, required for
18S rRNA synthesis
Nuclear protein, possibly involved in regulation of cation stress
responses and/or in the establishment of bipolar budding pattern
Essential protein involved in maturation of 18S rRNA; depletion
leads to inhibited pre-rRNA processing and reduced polysome
levels; localizes primarily to the nucleolus
Essential protein involved in ribosome biogenesis; putative
ATP-dependent RNA helicase of the DEAD-box protein family
U3 snoRNA); Something About Silencing 10; nuclear protein
involved in silencing
Essential ATP-dependent RNA helicase of the DEAD-box
protein family, involved in nonsense-mediated mRNA decay
and rRNA processing
involved in the maturation of 25S ribosomal RNA; ATPdependent RNA helicase
Ribosomal Like Protein 24
Protein of unknown function with similarity to human HMG1
and HMG2; localizes to the cytoplasm
Essential protein of unknown function
Regulator of Ty1 Transposition; Establishes Silent Chromatin;
involved in silencing
putative Upf1p-interacting protein; cytoplasmic factor required
for a late cytoplasmic assembly step of the 60S subunit
YGL099W
LSG1
YDL213C
NOP6
YPR110C
YBL054W
RPC40
None
YPL239W
YAR1
YDR465C
RMT2
YDR449C
UTP6
YNL114C
YJL010C
YDL208W
None
None
NHP2
YPR163C
TIF3
YLR051C
None
YJL033W
HCA4
YGR083C
GCD2
YPL044C
None
YLR276C
DBP9
YNR053C
NOG2
YDR365C
ESF1
YGL171W
ROK1
YDR083W
YOR004W
RRP8
None
YOR310C
NOP58
YNL022C
None
YNL110C
NOP15
YDL060W
TSR1
Putative GTPase involved in 60S ribosomal subunit biogenesis;
localized to the cytoplasm
Protein with similarity to hydrophilins, which are involved in the
adaptive response to hyperosmotic conditions; computational
analysis of large-scale protein-protein interaction data suggests a
possible role in rRNA processing
RNA polymerase subunit, common to RNA polymerase I and III
YAR1 encodes a 200-amino-acid protein with two ANK repeat
motifs and an acidic C terminus rich in PEST-like sequences
Arginine methyltransferase; ribosomal protein L12 is a substrate
HMG-like nuclear protein
Suppressor of translation mutants; Translation initiation factor
eIF-4B
Putative nucleolar DEAD box RNA helicase; high-copy number
suppression of a U14 snoRNA processing mutant suggests an
involvement in 18S rRNA synthesis
Delta subunit of the translation initiation factor eIF2B, the
guanine-nucleotide exchange factor for eIF2; activity
subsequently regulated by phosphorylated eIF2; first identified
as a negative regulator of GCN4 expression
ATP-dependent RNA helicase of the DEAD-box family
involved in biogenesis of the 60S ribosomal subunit
Putative GTPase that associates with pre-60S ribosomal subunits
in the nucleolus and is required for their nuclear export and
maturation
Nucleolar protein involved in pre-rRNA processing; depletion
causes severely decreased 18S rRNA levels
ATP-dependent RNA helicase of the DEAD box family;
required for 18S rRNA synthesis
None
Protein involved in pre-rRNA processing, 18S rRNA synthesis,
and snoRNA synthesis; component of the small subunit
processome complex, which is required for processing of pre18S rRNA
Constituent of 66S pre-ribosomal particles, involved in 60S
ribosomal subunit biogenesis; localizes to both nucleolus and
cytoplasm
Protein required for processing of 20S pre-rRNA in the
cytoplasm, associates with pre-40S ribosomal particles
YOR287C
None
YOR341W
RPA190
YNL061W
NOP2
YLR103C
CDC45
YKR079C
TRZ1
YBR247C
ENP1
YLR336C
SGD1
YDR120C
TRM1
YKL191W
DPH2
YDR097C
MSH6
YDR361C
BCP1
YNL002C
RLP7
YDL112W
TRM3
YNL227C
JJJ1
YNL113W
RPC19
YGR123C
PPT1
YGR162W
TIF4631
YBL028C
None
YMR229C
RRP5
YPL043W
NOP4
RNA polymerase I subunit alpha; largest subunit of RNA
polymerase I
Probable RNA m(5)C methyltransferase, essential for
processing and maturation of 27S pre-rRNA and large ribosomal
subunit biogenesis; localized to the nucleolus
DNA replication initiation factor; recruited to MCM pre-RC
complexes at origins of replication; promotes disengagement of
MCM from its anchor, Mcm10p, and recruits elongation
machinery
Protein associated with U3 and U14 snoRNAs, required for prerRNA processing and 40S ribosomal subunit synthesis; localized
in the nucleus and concentrated in the nucleolus
Suppressor of Glycerol Defect; may be involved in high
osmolarity signaling pathway
tRNA methyltransferase, localizes to both the nucleus and
mitochondrion to produce the modified base N2,N2dimethylguanosine in tRNAs in both compartments
Protein of unknown function, involved in diphtheria toxicity and
diphthamide biosynthesis, not essential for viability
Protein required for mismatch repair in mitosis and meiosis,
forms a complex with Msh2p to repair both single-base &
insertion-deletion mispairs; potentially phosphorylated by
Cdc28p
Essential protein involved in nuclear export of Mss4p, which is
a lipid kinase that generates phosphatidylinositol 4,5biphosphate and plays a role in actin cytoskeleton organization
and vesicular transport
Significant sequence similarity to RPL7B, but neither can
functionally replace the other. Does not correspond to any
ribosomal component identified so far, based on its biochemical
features; Protein with similarity to ribosomal proteins including
Rpl6p
2'-O-ribose methyltransferase, catalyzes the ribose methylation
of the guanosine nucleotide at position 18 of tRNAs
Protein that may function as a cochaperone, as suggested by the
presence of a DnaJ-like domain
RNA polymerase subunit, common to RNA polymerases I and
III
also called eIF4 (eIF-4) gamma; mRNA cap-binding protein
(eIF-4F), 150K subunit , highly homologous to Tif4632p,
homologs of mammalian p220
Part of small ribosomal subunit (SSU) processosome containing
U3 snoRNA); required for the synthesis of both 18S and 5.8S
rRNAs
Nucleolar protein, essential for processing and maturation of
YLR435W
TSR2
YMR309C
NIP1
YLL011W
SOF1
YKL083W
None
27S pre-rRNA and large ribosomal subunit biogenesis; contains
four RNA recognition motifs (RRMs)
Protein with a potential role in pre-rRNA processing
Protein required for nuclear import with some similarity to
Nsr1p, another protein involved in nuclear transport; ~100 kDa
cytoplasmic protein
Nucleolar protein, part of the small (ribosomal) subunit (SSU)
processosome that contains U3 snoRNA; has similarity to beta
subunits of G-proteins and the splicing factor Prp4p
Catalytic epsilon subunit of the translation initiation factor
eIF2B, the guanine-nucleotide exchange factor for eIF2; activity
subsequently regulated by phosphorylated eIF2; first identified
as a negative regulator of GCN4 expression
RNA polymerase III subunit C31; contains HMG-like Cterminal domain
Essential protein that binds ribosomal protein L11 and is
required for nuclear export of the 60S pre-ribosomal subunit
during ribosome biogenesis; mouse homolog shows altered
expression in Huntington's disease model mice
YDR211W
GCD6
YNL151C
RPC31
YOR294W
RRS1
YNL174W
None
YGR280C
PXR1
YGR264C
MES1
YCR072C
None
YPL217C
BMS1
YMR049C
ERB1
YLR175W
CBF5
YKL143W
LTV1
YGL111W
NSA1
YMR290W-A
YML018C
None
None
YER082C
UTP7
YDL050C
YOR243C
YIL091C
None
PUS7
None
pseudouridylates U2 snRNA at position 35
RLF2
Chromatin Assembly Complex, subunit 1: largest (p90) subunit
of three-subunit protein complex (yeast CAF-I) involved in
DNA-replication-linked nucleosome assembly. Homol. to p150
subunit human Chromatin Assembly Factor-I (CAF-I); p90
subunit of yeast Chromatin Assembly Factor-I (CAF-I)
YPR018W
Protein with a role in maturation of rRNAs and small nucleolar
RNAs; Protein required for cell viability
Methionyl-tRNA synthetase, forms a complex with glutamyltRNA synthetase (Ygl245wp) and Arc1p, which increases the
catalytic efficiency of both tRNA synthetases; also has a role in
nuclear export of tRNAs
GTP-binding protein required for processing of 35S pre-rRNA
at sites A0,
Protein required for maturation of the 25S and 5.8S ribosomal
RNAs; homologous to mammalian Bop1
major low affinity 55 kDa Centromere/microtubule binding
protein
Protein required for growth at low temperature
ribosomal subunit biogenesis
YOL124C
None
YOL010W
RCL1
YJL122W
None
YJL050W
MTR4
YNL299W
TRF5
YHR149C
SKG6
YNR054C
ESF2
YHR196W
UTP9
YER126C
NSA2
YOR047C
STD1
YOR119C
RIO1
YNL023C
FAP1
YIL127C
YDL167C
YPR136C
None
NRP1
None
YPR144C
NOC4
YOR094W
ARF3
YOR078W
BUD21
YNL248C
RPA49
YGR128C
UTP8
YLR063W
None
YOL097C
WRS1
YLR409C
UTP21
YHR065C
RRP3
RNA terminal phosphate cyclase-like protein involved in rRNA
processing at sites A0, A1, and A2; does not possess detectable
RNA cyclase activity
Dead-box family ATP dependent helicase required for mRNA
export from the nucleus; co-factor of the exosome complex,
required for 3' end formation of 5.8S rRNA
TRF4 homolog; TRF4/5 function is required for proper mitosis;
exhibits homology to Trf4p and Top1p
Protein of unknown function found in the bud tip and bud neck,
ribosomal subunit biogenesis
Essential protein that plays a role in cell cycle progression, has
similarity to C. elegans ZK632.3 protein
Protein that binds to Fpr1p (FKBP12), conferring rapamycin
resistance by competing with rapamycin for Fpr1p binding; has
similarity to putative transcription factors, including D.
melanogaster shuttle craft and human NFX1
Protein of unknown function, rich in asparagine residues
Nucleolar protein, forms a complex with Nop14p that mediates
maturation and nuclear export of 40S ribosomal subunits
GTP-binding ADP-ribosylation factor
Component of small ribosomal subunit (SSU) processosome that
contains U3 snoRNA; originally isolated as bud-site selection
mutant that displays a random budding pattern
Nucleolar protein required for export of tRNAs from the
nucleus; also copurifies with the small subunit (SSU)
Cytoplasmic tryptophanyl-tRNA synthetase, aminoacylates
tryptophanyl-tRNA
Possible U3 snoRNP protein involved in maturation of pre-18S
rRNA, based on computational analysis of large-scale proteinprotein interaction data
Required for maturation of the 35S primary transcript of prerRNA and is required for cleavages leading to mature 18S RNA;
RRP3 is a DEAD box gene homologous to eIF-4a which
encodes an RNA-dependent ATPase possessing helicase activity
YMR290C
HAS1
YHR088W
RPF1
YLL008W
DRS1
YDR312W
SSF2
YDR152W
GIR2
YOR001W
RRP6
YER049W
None
YFR001W
LOC1
YOR146W
None
YNL068C
FKH2
YNL308C
KRI1
YNL164C
IBD2
YKR092C
SRP40
YAL036C
RBG1
YGR155W
CYS4
YDR101C
ARX1
YBR267W
REI1
YAL059W
ECM1
YLR196W
PWP1
YPL158C
None
YPL086C
ELP3
which is not specific for RNA
Putative ATP-dependent RNA helicase; localizes to both the
nuclear periphery and nucleolus; highly enriched in nuclear pore
complex fractions
Nucleolar protein involved in the assembly of the large
ribosomal subunit; contains a sigma(70)-like motif, which is
thought to bind RNA
Nucleolar DEAD-box protein required for ribosome assembly
and function, including synthesis of 60S ribosomal subunits
high copy suppressor of G beta subunit temperature sensitive
mutation; possibly involved in mating
RWD domain containing protein of unknown function
Exonuclease component of the nuclear exosome; contributes to
the quality-control system that retains and degrades aberrant
mRNAs in the nucleus
Nuclear protein involved in asymmetric localization of ASH1
mRNA; binds double-stranded RNA in vitro
silencing at HML and HMR; potential Cdc28p substrate
Essential nucleolar protein required for 40S ribosome
biogenesis; physically and functionally interacts with Krr1p
Component of the BUB2-dependent spindle checkpoint
pathway, interacts with Bfa1p and functions upstream of Bub2p
and Bfa1p
Suppressor of mutant AC40 subunit of RNA polymerase I and
III; nucleolar protein that is immunologically and structurally
related to rat Nopp140, a nonribosomal protein of the nucleolus
and coiled bodies.
GTPase, interacts with ribosomes, has similarity to Xenopus
GTP-binding protein DRG
Cystathionine beta-synthase, catalyzes the first committed step
of transsulfuration in cysteine biosynthesis
None
Protein of unknown function involved in bud growth in the
mitotic signaling network; proposed negative regulator of
Swe1p and Gin4p; contains dispersed C2H2 zinc finger domains
Protein of unknown function, localized in the nucleoplasm and
the nucleolus, genetically interacts with MTR2 in 60S ribosomal
protein subunit export
Protein with periodic trytophan residues that resembles members
of beta-transducin superfamily because of presence of WD-40
repeats; similar to beta-transducin superfamily
Histone acetyltransferase subunit of the Elongator complex,
which is a component of the RNA polymerase II holoenzyme;
activity is directed specifically towards histones H3 and H4;
disruption confers resistance to K. lactis zymotoxin
YIR012W
SQT1
YHR148W
IMP3
YKL172W
EBP2
YDR060W
MAK21
YGL078C
DBP3
YMR269W
YDL063C
None
None
YPR112C
MRD1
YOR206W
NOC2
YGR200C
ELP2
YIL096C
YOR359W
None
VTS1
YLR401C
DUS3
YKL113C
RAD27
YCR057C
PWP2
YFL023W
BUD27
YPL146C
YIR026C
None
YVH1
YLL034C
RIX7
Protein involved in a late step of 60S ribosomal subunit
assembly or modification; contains multiple WD repeats;
interacts with Qsr1p in the two-hybrid system
Component of the SSU processome, which is required for pre18S rRNA processing, essential protein that interacts with
Mpp10p and mediates interactions of Imp4p and Mpp10p with
U3 snoRNA
Essential protein required for the maturation of 25S rRNA and
60S ribosomal subunit assembly, localizes to the nucleolus
Protein required for large (60S) ribosomal subunit biogenesis;
involved in nuclear export of pre-ribosomes; required for
maintenance of dsRNA virus; homolog of human CAATTbinding protein
involved in ribosomal biogenesis
Essential conserved protein that associates with 35S precursor
rRNA and is required for its initial processing at the A(0)-A(2)
cleavage sites, shows partial nucleolar localization, contains five
consensus RNA-binding domains
Protein that forms a nucleolar complex with Mak21p that binds
to 90S and 66S pre-ribosomes, as well as a nuclear complex
with Noc3p that binds to 66S pre-ribosomes; both complexes
mediate intranuclear transport of ribosomal precursors
None
Dihydrouridine synthase, member of a widespread family of
conserved proteins including Smm1p, Dus1p, and Dus4p;
contains a consensus oleate response element (ORE) in its
promoter region
5' to 3' exonuclease, 5' flap endonuclease, required for Okazaki
fragment processing and maturation as well as for long-patch
base-excision repair; member of the S. pombe RAD2/FEN1
family
U3 snoRNA); Eight WD-repeats with homology with G protein
beta subunits flanked by nonhomologous N-terminal and Cterminal extensions; regulatory protein
Protein involved in bud-site selection, nutrient signaling, and
gene expression controlled by the TOR kinase; diploid mutants
display a random budding pattern instead of the wild-type
bipolar pattern
Putative ATPase of the AAA family, required for export of preribosomal large subunits from the nucleus; distributed between
the nucleolus, nucleoplasm, and nuclear periphery depending on
growth conditions
(45) MODULE 52
YHR030C
SLT2
YDL170W
UGA3
Genotype regulators
NUC1(1,2) CBP1(6,3) PEX2(1,6) YJL211C OPT1(3,6)
YJL213W HXT8(93,12) YJL215C YJL216C YJL217W
YJL218W HXT9(12,50) YJL220W FSP2(4,32) VTH2(323,435)
TUB2(1,1) YPT1(0,1) ACT1(3,5) YFL040W FET5(4,1)
YFL041W-A YFL042C YFL043C YOD1(1,0) SEC53(0,2)
FMP32(1,3) RGD2(5,3) EMP47(4,3) YFL049W ALR2(19,15)
YFL051C YFL052W
M10_22213_34098
M6_38648_48224
Module genes
YFL052W
YFL054C
None
None
YFL053W
DAK2
YDL244W
THI13
YNL331C
AAD14
YFL056C
AAD6
YFL055W
AGP3
(46) MODULE 53
YPL230W
None
YLL019C
KNS1
YPL230W
None
YOL113W
SKM1
YLR150W
STM1
YLL019C
KNS1
Dihydroxyacetone kinase, required for detoxification of
dihydroxyacetone (DHA); involved in stress adaptation
Protein involved in synthesis of the thiamine precursor
hydroxymethylpyrimidine (HMP); member of a subtelomeric
gene family including THI5, THI11, THI12, and THI13
chrysosporium aryl-alcohol dehydrogenase, involved in the
oxidative stress response
Low-affinity amino acid permease, may act to supply the cell
with amino acids as nitrogen source in nitrogen-poor conditions;
transcription is induced under conditions of sulfur limitation
tyrosine residues
Cla4p
tyrosine residues
Module genes
YOL084W
PHM7
YHR140W
None
YDL046W
NPC2
YLR289W
GUF1
YOR028C
CIN5
YNL173C
MDG1
YHR034C
PIH1
YGR086C
PIL1
YDR406W
PDR15
YOR031W
CRS5
YOR161C
PNS1
YJL016W
YHR033W
YNR036C
YGL226W
None
None
None
None
YOR125C
CAT5
YPR149W
NCE102
YOL053W
YMR031C
None
None
YDL049C
KNH1
YIL101C
XBP1
Protein of unknown function, expression is regulated by
phosphate levels; green fluorescent protein (GFP)-fusion protein
localizes to the cell periphery and vacuole
Putative homolog of human NPC2/He1, which is a cholesterolbinding protein whose deficiency causes Niemann-Pick type C2
disease involving retention of cholesterol in lysosomes
Mitochondrial GTPase of unknown function, similar to E. coli
elongation factor-type GTP-binding protein LepA and to
LK1236.1 from Caenorhabditis elegans
Basic leucine zipper transcriptional factor of the yAP-1 family
that mediates pleiotropic drug resistance and salt tolerance;
localizes constitutively to the nucleus
Plasma membrane protein involved in G-protein mediated
pheromone signaling pathway; overproduction suppresses bem1
mutations
Protein possibly involved in protein synthesis
Long chain base-responsive inhibitor of protein kinases Phk1p
and Phk2p, acts along with Lsp1p to down-regulate heat stress
resistance via regulation of the Pkc1p and Ypk1p pathways;
phosphorylated by Phk1p and Phk2p
ATP binding cassette (ABC) transporter of the plasma
membrane; general stress response factor implicated in cellular
detoxification; target of Pdr1p, Pdr3p and Pdr8p transcription
regulators; promoter contains a PDR responsive element
Copper-binding metallothionein, required for wild-type copper
resistance
Protein of unknown function; has similarity to Torpedo
californica tCTL1p, which is postulated to be a choline
transporter, neither null mutation nor overexpression affects
choline transport
may encode a protein involved in one or more monoxygenase or
hydroxylase steps of ubiquinone biosynthesis
involved in secretion of proteins that lack classical secretory
signal sequences; Involved in secretion of proteins that lack
classical secretory signal sequences
Protein with similarity to Kre9p, which is involved in cell wall
beta 1,6-glucan synthesis; overproduction suppresses growth
defects of a kre9 null mutant
YNL100W
YOL047C
None
None
YKL150W
MCR1
YKL062W
MSN4
YLL020C
YOR062C
YMR244C-A
None
None
None
YBR091C
MRS5
YHR044C
DOG1
YIL087C
None
YGR230W
BNS1
YPL161C
BEM4
YHL024W
RIM4
YER097W
YNL234W
YCR083W
YMR031W-A
None
None
TRX3
None
YER062C
HOR2
YGL208W
SIP2
YDR216W
ADR1
YGR243W
YMR254C
FMP43
None
YJR127C
ZMS1
YJR119C
None
Mitochondrial NADH-cytochrome b5 reductase, involved in
ergosterol biosynthesis
Essential protein of the inner mitochondrial membrane,
peripherally localized; component of the TIM22 complex, which
is a a twin-pore translocase that mediates insertion of numerous
multispanning inner membrane proteins
2-deoxyglucose-6-phosphate phosphatase, similar to Dog2p,
member of a family of low molecular weight phosphatases;
confers 2-deoxyglucose resistance when overexpressed, in vivo
substrate has not yet been identified
Protein with some similarity to Spo12p; overexpression
bypasses need for Spo12p, but not required for meiosis
Protein involved in establishment of cell polarity and bud
emergence; interacts with the Rho1p small GTP-binding protein
and with the Rho-type GTPase Cdc42p
Regulator of IMe2 expression; RNA-binding protein of the
RRM class (putative)
mitochondrial thioredoxin
One of two redundant DL-glycerol-3-phosphatases
(RHR2/GPP1 encodes the other) involved in glycerol
biosynthesis; induced in response to hyperosmotic stress and
oxidative stress, and during the diauxic transition
Member of a family of proteins, including Sip1p and Gal83p,
that interact with Snf1p and Snf4p and are involved in the
response to glucose starvation; component of Snf1 protein
complex involved in response to glucose starvation
Positive transcriptional regulator, controls the expression of
ADH2, peroxisomal protein genes, and genes required for
ethanol, glycerol, and fatty acid utilization
The authentic, non-tagged protein was localized to mitochondria
Zinc-finger protein that localizes to the nucleus, putative
transcriptional regulator of ALD6
(47) MODULE 54
YGR233C
PHO81
YOL113W
SKM1
YER177W
BMH1
YBR083W
TEC1
YDL230W
Genotype regulators
PTP1
Cyclin-dependent kinase (CDK) inhibitor, regulates Pho80pPho85p and Pcl7p-Pho85p cyclin-CDK complexes in response
to phosphate levels; required for derepression of PHO5;
transcriptionally regulated by Pho4p and Pho2p
Cla4p
others
transcription factor of the TEA/ATTS DNA-binding domain
family, regulator of Ty1 expression
YML116W-A NAB6(7,1) YML117W-A NGL3(3,3)
YML119W NDI1(1,1) GTR1(0,50) YML122C PHO84(2,48)
TUB3(8,0) YML125C ERG13(0,0) RSC9(0,0)
M13_27644_28694
Module genes
YFR042W
None
YKR091W
SRL3
YMR245W
YDL118W
None
None
YBR193C
MED8
YAL064W
YJL032W
None
None
YOL133W
HRT1
YKL158W
None
YDR256C
CTA1
YPR130C
YGR137W
YDR327W
YOR024W
YIR020C
YJL119C
None
None
None
None
None
None
YPL169C
MEX67
YDR223W
CRF1
Cytoplasmic protein that, when overexpressed, suppresses the
lethality of a rad53 null mutation; potential Cdc28p substrate
Member of RNA Polymerase II transcriptional regulation
mediator; Stoichiometric member of mediator complex
RING finger containing subunit of Skp1-Cullin-F-box ubiquitin
protein ligases (SCF); required for Gic2p, Far1p, Sic1p and
Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating
enzyme or E2) and Cdc53p (a cullin) subunits of SCF
Catalase A, breaks down hydrogen peroxide in the peroxisomal
matrix formed by acyl-CoA oxidase (Pox1p) during fatty acid
beta-oxidation
Involved in nuclear mRNA export, binds both poly(A); a
poly(A)+RNA binding protein
Protein of unknown function, potentially phosphorylated by
Cdc28p
YGR188C
BUB1
YNL238W
KEX2
YCL001W-A
YNL211C
None
None
YOR190W
SPR1
YJL022W
None
YFL020C
PAU5
YPL200W
CSM4
checkpoint gene involved in permitting entry into mitosis
depending upon the assembly state of microtubules;
Serine/threonine protein kinase required for cell cycle arrest in
response to loss of microtubule function
Subtilisin-like protease (proprotein convertase), a calciumdependent serine protease involved in the activation of
proproteins of the secretory pathway
Sporulation regulated genes; sporulation-specific exo-1,3-betaglucanase
Protein required for accurate chromosome segregation during
meiosis
(48) MODULE 55
YDR195W
REF2
YFL031W
HAC1
YGL037C
PNC1
YJL103C
Module genes
YNL140C
None
None
YPR111W
DBF20
YFL033C
RIM15
YAL029C
MYO4
YLR124W
YDR219C
None
None
YML124C
TUB3
YGL178W
MPT5
snoRNA maturation
synthesis
nicotinamidase
Ser/Thr kinase involved in late nuclear division, one of the
mitotic exit network (MEN) proteins; necessary for the
execution of cytokinesis
RIM15 is glucose-repressed; RIM15 is required for IME2
expression; Trehalose-associated protein kinase related to S.
pombe cek1+
Required for mother-specific HO expression, for the bud tip
localization of ASH1 and IST2 mRNA; facilitates growth and
orientation of ER tubules along with She3p; myosin
Alpha-tubulin; associates with beta-tubulin (Tub2p) to form
tubulin dimer, which polymerizes to form microtubules;
expressed at lower level than Tub1p
Protein that specifically binds to mRNAs encoding chromatin
modifiers and spindle pole body components; has roles in
longevity, in maintenance of cell wall integrity, and in
sensitivity to and recovery from pheromone arrest
Purine-cytosine permease, mediates purine (adenine, guanine,
and hypoxanthine) and cytosine accumulation
Copper-binding transcription factor; activates transcription of
the metallothionein genes CUP1-1 and CUP1-2 in response to
elevated copper concentrations
Similar to human tumor suppressor gene known as TEP1,
MMAC1 and PTEN1; Putative protein tyrosine phosphatase
YER056C
FCY2
YGL166W
CUP2
YNL128W
TEP1
YJL097W
YKL147C
YOR213C
YHR021W-A
YLR422W
YDR431W
None
None
SAS5
ECM12
None
None
Protein involved in silencing at telomeres, HML, and HMR
YOR237W
HES1
Protein implicated in the regulation of ergosterol biosynthesis;
one of a seven member gene family with a common essential
function and non-essential unique functions; similar to human
oxysterol binding protein (OSBP)
YNR025C
None
YNR072W
HXT17
YEL017W
GTT3
YEL041W
None
YLR411W
CTR3
YMR228W
MTF1
YKR015C
YJL216C
YDR370C
YIL170W
None
None
None
None
YMR013C
SEC59
YPL132W
COX11
YGL132W
None
YBR240C
THI2
transporter family members, expression is repressed by high
levels of glucose
Protein of unknown function with a possible role in glutathione
metabolism, as suggested by computational analysis of largescale protein-protein interaction data; GFP-fusion protein
localizes to the nuclear periphery
High-affinity copper transporter of the plasma membrane, acts
as a trimer; gene is disrupted by a Ty2 transposon insertion in
many laboratory strains of S. cerevisiae
Mitochondrial RNA polymerase sigma-like specificity factor
required for promoter recognition, interacts with mitochondrial
core polymerase Rpo41p, imported into mitochondria via a
novel process requiring most of the Mtf1p sequence
Membrane protein that catalyzes the CTP-mediated
phosphorylation of dolichol, the terminal step in dolichyl
monophosphate (Dol-P) biosynthesis; required for viability,
normal rates of lipid intermediate synthesis, and protein Nglycosylation
Mitochondrial membrane protein required for assembly of active
cytochrome c oxidase, probably involved in insertion of Cu(B)
and magnesium
Zinc finger protein of the Zn(II)2Cys6 type, probable
transcriptional activator of thiamine biosynthetic genes
(49) MODULE 56
YCL055W
KAR4
YGR156W
Genotype regulators
PTI1
NEO1(0,4) DFG10(4,6) PCL7(1,2) MMF1(1,2) RPL34B(13,11)
RHR2(0,7) YIL054W YIL055C YIL056W YIL057C YIL058W
YIL059C YIL060W SNP1(3,132) ARC15(0,2) YRB2(3,1)
YIL064W FIS1(0,1) RNR3(2,6) YIL066W-A YIL067C
SEC6(0,0) YIL068W-A RPS24B(1,2) MAM33(0,0) PCI8(0,0)
YIL071W-A HOP1(1,9) SPO22(218,0) SER33(1,0) RPN2(0,0)
SEC28(0,4) YIL077C THS1(2,4) AIR1(3,4) YIL080W
YIL082W YIL082W-A
M9_214482_254745
Module genes
YIL080W
YIL082W-A
YIL049W
YIL082W
(50) MODULE 57
None
None
DFG10
None
YCR040W
MATALPHA1
YCL055W
KAR4
Protein of unknown function, involved in filamentous growth
Module genes
YFL025C
BST1
YCR097W
HMRA1
YGL033W
HOP2
YIL015W
BAR1
YJL170C
ASG7
Protein that negatively regulates COPII vesicle formation;
functionally complements mammalian PGAP1, which is a GPI
inositol-deacylase involved in GPI maturation; negative
regulator of COPII vesicle formation
Silenced copy of A1, encoding a homeobox-domain containing
corepressor that interacts with Alpha2p to repress haploidspecific gene transcription in diploid cells
Meiosis-specific protein that localizes to chromosomes,
preventing synapsis between nonhomologous chromosomes and
ensuring synapsis between homologs; complexes with Mnd1p to
promote homolog pairing and meiotic double-strand break repair
Aspartyl protease secreted into the periplasmic space of mating
type a cells, cleaves and inactivates alpha factor allowing cells
to recover from alpha-factor-induced cell cycle arrest
an a-specific gene that is induced to a higher expression level by
alpha factor; An a-specific gene that is induced to a higher
expression level by alpha factor
YHR178W
YOL025W
STB5
LAG2
YLR288C
MEC3
YNL145W
MFA2
YFL027C
GYP8
YGL032C
AGA2
YFL026W
STE2
YCR097W-A
None
YKL209C
STE6
YDR461W
(51) MODULE 58
MFA1
YFL031W
HAC1
YGL166W
CUP2
YGR014W
MSB2
YKL126W
YPK1
YPL026C
SKS1
YGL166W
CUP2
YKL126W
YPK1
Module genes
YGL074C
YML032C-A
YLR374C
YBL108W
YLL037W
None
None
None
None
None
binds Sin3p in two-hybrid assay; Zinc finger (6-Cys)
affects longevity; involved in determination of longevity
Involved in checkpoint control and DNA repair; forms a clamp
with Rad17p and Ddc1p that is loaded onto partial duplex DNA;
DNA damage checkpoint protein
lipopeptide mating pheromone; mating a-factor pheromone
precursor
GTPase-activating protein for yeast Rab family members; Ypt1p
is the preferred in vitro substrate but also acts on Sec4p, Ypt31p
and Ypt32p; involved in the regulation of ER to Golgi vesicle
transport
Adhesion subunit of a-agglutinin of a-cells, C-terminal sequence
acts as a ligand for alpha-agglutinin (Sag1p) during
agglutination, modified with O-linked oligomannosyl chains,
linked to anchorage subunit Aga1p via two disulfide bonds
alpha-factor pheromone receptor; seven-transmembrane domain
protein
ABC transporter, glycoprotein, component of a-factor secretory
pathway
synthesis
76.5 kDa Serine/threonine protein kinase with similarity to
protein kinase C, is 90% identical to Ypk2p
YDR455C
YFR056C
YDL062W
YDR187C
None
None
None
None
YDR538W
PAD1
YDL026W
YPR092W
YLR140W
YML117W-A
YLR349W
None
None
None
None
None
YMR159C
ATG16
YGL239C
YJR079W
YGR064W
YLR169W
YKL162C-A
YBL073W
YDR290W
YNL205C
YJL182C
YGR190C
YKL037W
YCL023C
YMR194C-A
YLR122C
YLR202C
YJL120W
YJL169W
YPR142C
YMR119W-A
YBR124W
YDR199W
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
YAR031W
PRM9
YGR114C
YML058C-A
YGR291C
YMR324C
YBR100W
None
None
None
None
None
Phenylacrylic acid decarboxylase, confers resistance to cinnamic
acid, decarboxylates aromatic carboxylic acids to the
corresponding vinyl derivatives
Protein that interacts with the Atg12p-Atg5p conjugate during
formation of the pre-autophagosomal structure; essential for
autophagy
Pheromone-regulated protein with 3 predicted transmembrane
segments and an FF sequence, a motif involved in COPII
binding
YEL059C-A
SOM1
YKL118W
YGL072C
YBL096C
None
None
None
YDL232W
OST4
YDL152W
YHR079C-B
YBR099C
YCR001W
YLR428C
YGR290W
YDR445C
None
None
None
None
None
None
None
YPR151C
SUE1
YCR062W
YLR279W
YML100W-A
YNL235C
YJL211C
None
None
None
None
None
YER060W-A
FCY22
YLR236C
YGL165C
YJL015C
YIL141W
YNL203C
YOR282W
YNL226W
YJL018W
YDR366C
YOR013W
YER091C-A
YLR281C
YHR145C
None
None
None
None
None
None
None
None
None
None
None
None
None
YML094W
GIM5
YPR039W
YGR039W
(52) MODULE 59
None
None
Protein whose overexpression suppresses the imp1 mutation,
may be required for the function of the Imp1p mitochondrial
inner membrane peptidase and/or the protein sorting machinery
Subunit of the oligosaccharyltransferase complex of the ER
lumen, which catalyzes aspargine-linked glycosylation of newly
synthesized proteins; type I membrane protein of 36 residues
that binds Stt3p and Ost3p together in a subcomplex
Mitochondrial protein required for degradation of unstable
forms of cytochrome c
Putative purine-cytosine permease, very similar to Fcy2p but
cannot substitute for its function
Prefoldin subunit 5; putative homolog of subunit 5 of bovine
prefoldin, a chaperone comprised of six subunits; bovine
prefoldin subunit 5 homolog (putative)
Genotype regulators
PHM7(7,11) YOL085C YOL085W-A ADH1(4,8) YOL086W-A
YOL087C MPD2(4,6) HAL9(15,4) MSH2(2,3) SPO21(3,6)
YOL092W TRM10(5,4) RFC4(1,4) HMI1(5,1) COQ3(2,0)
WRS1(1,3) YOL097W-A YOL098C YOL099C PKH2(7,6)
IZH4(0,5) TPT1(2,3) ITR2(0,365) NDJ1(4,456) WSC3(6,2)
YOL106W YOL107W INO4(0,1) ZEO1(1,3) SHR5(1,3)
YOL111C MSB4(2,0) SKM1(9,2) YOL114C TRF4(4,4)
MSN1(2,5)
M15_108577_154309
Module genes
YOL113W
SKM1
YOL104C
NDJ1
Cla4p
Meiosis-specific telomere protein, required for bouquet
formation, effective homolog pairing, ordered cross-over
distribution (interference), sister chromatid cohesion at meiotic
telomeres, and segregation of small chromosomes
(53) MODULE 61
Genotype regulators
PHM7(7,11) YOL085C YOL085W-A ADH1(4,8) YOL086W-A
YOL087C MPD2(4,6) HAL9(15,4) MSH2(2,3) SPO21(3,6)
YOL092W TRM10(5,4) RFC4(1,4) HMI1(5,1) COQ3(2,0)
WRS1(1,3) YOL097W-A YOL098C YOL099C PKH2(7,6)
IZH4(0,5) TPT1(2,3) ITR2(0,365) NDJ1(4,456) WSC3(6,2)
YOL106W YOL107W INO4(0,1) ZEO1(1,3) SHR5(1,3)
YOL111C MSB4(2,0) SKM1(9,2) YOL114C TRF4(4,4)
MSN1(2,5)
M15_108577_154309
Module genes
YOL091W
SPO21
YLL028W
TPO1
(54) MODULE 62
YBR125C
PTC4
YBR140C
IRA1
Module genes
YOR304C-A
None
YER044C-A
MEI4
YOR041C
SRF5
YBR301W
DAN3
Component of the meiotic outer plaque of the spindle pole body,
involved in modifying the meiotic outer plaque that is required
prior to prospore membrane formation
Proton-motive-force-dependent multidrug transporter of the
major facilitator superfamily; able to transport eight different
compounds, including polyamines, quinidine, cycloheximide,
and nystatin; involved in excess spermidine detoxification
Functions in early recombination; mRNA is meiosis-specific
and has 88 bp intron at 5' end spliced independently of MER1.
ORF overlaps the uncharacterized gene CUE5; deletion in cyr1
mutant results in loss of stress resistance
Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p,
YLL003W
YML010W-A
(55) MODULE 63
SFI1
None
YBR274W
CHK1
YPL086C
ELP3
YGR288W
MAL13
YGR123C
PPT1
YGL037C
PNC1
YHR122W
None
YGL121C
GPG1
Module genes
YBR162W-A
YSY6
YBR060C
ORC2
YBR075W
None
YBR163W
DEM1
YBR112C
CYC8
YBR281C
None
YBL024W
NCL1
YBL082C
RHK1
YBL032W
HEK2
YBL008W
HIR1
and Tir4p; expressed under anaerobic conditions, completely
repressed during aerobic growth
None
Histone acetyltransferase subunit of the Elongator complex,
which is a component of the RNA polymerase II holoenzyme;
activity is directed specifically towards histones H3 and H4;
disruption confers resistance to K. lactis zymotoxin
nicotinamidase
Gpa2p
Protein that participates in secretory pathway
Subunit of the origin recognition complex, which directs DNA
replication by binding to replication origins and is also involved
in transcriptional silencing; may be phosphorylated by Cdc28p
Protein of unknown function, shows similarity to RNAprocessing protein Pta1p
General transcriptional co-repressor, acts together with Tup1p;
also acts as part of a transcriptional co-activator complex that
recruits the SWI/SNF and SAGA complexes to promoters
Nuclear protein 1, similar to NOP2 and human proliferation
associated nucleolar protein p120; Probable proliferating-cell
nucleolar antigen (human p120)
Dolichol-P-Man dependent alpha(1-3) mannosyltransferase,
involved in the synthesis of dolichol-linked oligosaccharide
donor for N-linked glycosylation of proteins
RNA binding protein with similarity to hnRNP-K that localizes
to the cytoplasm and to subtelomeric DNA; required for the
proper localization of ASH1 mRNA; involved in the regulation
of telomere position effect and telomere length
Non-essential transcriptional corepressor involved in the cell
cycle-regulated transcription of histone H2A, H2B, H3 and H4
genes; contributes to nucleosome formation, heterochromatic
gene silencing, and formation of functional kinetochores
YOR116C
RPO31
YBR004C
FMP44
YBR245C
ISW1
YBR261C
None
YBR069C
TAT1
YBL020W
RFT1
YBL004W
UTP20
YBL085W
BOI1
YBL077W
None
YBR065C
ECM2
YPR080W
TEF1
YBL034C
STU1
YBL018C
POP8
YBL081W
None
YBR061C
TRM7
YBR125C
PTC4
YBR029C
CDS1
YBR252W
DUT1
YBR244W
GPX2
YBR084W
MIS1
YBL014C
RRN6
YBR017C
KAP104
RNA polymerase III large subunit
mitochondria
Member of the imitation-switch (ISWI) class of ATP-dependent
chromatin remodeling complexes; ATPase that forms a complex
with Ioc2p and Ioc4p to regulate transcription elongation, and a
complex with Ioc3p to repress transcription initiation
Amino acid transport protein for valine, leucine, isoleucine, and
tyrosine
Flippase, essential integral membrane protein that is required for
translocation of Man5GlcNac2-PP-Dol from the cytoplasmic
side to the lumenal side of the ER membrane; mutation is
suppressed by expression human p53 protein
Possible snoRNA-binding protein, based on computational
analysis of large-scale protein-protein interaction data
Protein implicated in polar growth, functionally redundant with
Boi2p; interacts with bud-emergence protein Bem1p; contains
an SH3 (src homology 3) domain and a PH (pleckstrin
homology) domain
Pre-mRNA splicing factor, facilitates the cooperative formation
of U2/U6 helix II in association with stem II in the spliceosome,
function may be regulated by Slu7p
functions in the binding reaction of aminoacyl-tRNA (AAtRNA) to ribosomes; translational elongation factor EF-1 alpha
Component of the mitotic spindle that binds to interpolar
microtubules and plays an essential role in their ability to
provide an outward force on the spindle poles
Subunit of both RNase MRP, which cleaves pre-rRNA, and
nuclear RNase P, which cleaves tRNA precursors to generate
mature 5' ends
2'-O-ribose methyltransferase, methylates the 2'-O-ribose of
nucleotides at positions 32 and 34 of the tRNA anticodon loop
CDP-diacylglycerol synthase, CTP-phosphatidic acid
cytidylyltransferase, CDP-diglyceride synthetase
dUTPase, catalyzes the hydrolysis of dUTP to dUMP and PPi
and thereby prevents the incorporation of uracil into DNA
during replication
Phospholipid hydroperoxide glutathione peroxidase induced by
glucose starvation that protects cells from phospholipid
hydroperoxides and nonphospholipid peroxides during oxidative
stress
mitochondrial C1-tetrahydroflate synthase
involved in the transcription of 35S rRNA genes by RNA
polymerase I; member of yeast Pol I core factor (CF) also
composed of Rrn11p, Rrn7p and TATA-binding protein
Transportin, cytosolic karyopherin beta 2 involved in delivery of
YBR121C
GRS1
YBR266C
None
YBL091C
MAP2
YBL067C
YBL083C
YBL041W
YBL009W
UBP13
None
PRE7
None
YBR101C
FES1
YBR166C
TYR1
YBR162C
TOS1
YBR154C
RPB5
YBR200W
BEM1
YNL273W
YBR089W
TOF1
None
YBL035C
POL12
YBL051C
PIN4
YBR084C-A
RPL19A
YGL014W
YBL062W
PUF4
None
YBR034C
HMT1
YBR153W
RIB7
YBR233W
PBP2
heterogeneous nuclear ribonucleoproteins to the nucleoplasm,
binds rg-nuclear localization signals on Nab2p and Hrp1p, plays
a role in cell-cycle progression
Cytoplasmic and mitochondrial glycyl-tRNA synthase that
ligates glycine to the cognate anticodon bearing tRNA;
transcription termination factor that may interact with the 3'-end
of pre-mRNA to promote 3'-end formation
Methionine aminopeptidase, catalyzes the cotranslational
removal of N-terminal methionine from nascent polypeptides;
function is partially redundant with that of Map1p
Putative ubiquitin-specific protease
20S proteasome beta-type subunit
Hsp70 (Ssa1p) nucleotide exchange factor, cytosolic homolog of
Sls1p, which is the nucleotide exchange factor for BiP (Kar2p)
in the endoplasmic reticulum
Step of tyrosine biosynthesis pathway; Prephenate
dehydrogenase (NADP+)
Target of SBF
I, II, and III
Protein containing SH3-domains, involved in establishing cell
polarity and morphogenesis; functions as a scaffold protein for
complexes that include Cdc24p, Ste5p, Ste20p, and Rsr1p
Protein that interacts with topoisomerase I
Subunit of the DNA polymerase alpha-primase complex,
required for the initiation of DNA replication during mitotic
DNA synthesis and premeiotic DNA synthesis
Protein involved in G2/M phase progression and response to
DNA damage, interacts with Rad53p; contains an RNA
recognition motif, a nuclear localization signal, and several
SQ/TQ cluster domains; hyperphosphorylated in response to
DNA damage
Protein component of the large (60S) ribosomal subunit, nearly
identical to Rpl19Bp and has similarity to rat L19 ribosomal
protein; rpl19a and rpl19b single null mutations result in slow
growth, while the double null mutation is lethal
Nuclear SAM-dependent mono- and asymmetric arginine
dimethylating methyltransferase that modifies hnRNPs,
including Npl3p and Hrp1p, thus facilitating nuclear export of
these proteins; required for viability of npl3 mutants
Diaminohydroxyphoshoribosylaminopyrimidine deaminase;
catalyzes the second step of the riboflavin biosynthesis pathway
RNA binding protein with similarity to mammalian
heterogeneous nuclear RNP K protein, involved in the
YBR073W
RDH54
YBR283C
SSH1
YBR195C
MSI1
YBL076C
ILS1
YBR079C
RPG1
YBL079W
NUP170
YBR243C
ALG7
YBR219C
YBR194W
YBR098W
YBL052C
YBL036C
YBR063C
None
SOY1
MMS4
SAS3
None
None
YBR021W
FUR4
YBR143C
SUP45
YBR078W
ECM33
YBR094W
YBR242W
YBR074W
None
None
None
YBL027W
RPL19B
YBR023C
CHS3
YBR142W
MAK5
regulation of telomere position effect and telomere length
genetic interaction with DMC1; Putative helicase similar to
RAD54
Sec61p homolog involved in co-translational pathway of protein
transport
Subunit of chromatin assembly factor I (CAF-I), regulates the
RAS/cAMP pathway via sequestration of Npr1p kinase;
localizes to the nucleus and cytoplasm; homologous to human
retinoblastoma binding proteins RbAp48 and RbAp46
Cytoplasmic isoleucine-tRNA synthetase, target of the G1specific inhibitor reveromycin A
Subunit of the core complex of translation initiation factor
3(eIF3), essential for translation; part of a subcomplex (Prt1pRpg1p-Nip1p) that stimulates binding of mRNA and
tRNA(i)Met to ribosomes
Abundant subunit of the nuclear pore complex (NPC), required
for proper localization of specific nucleoporins within the NPC,
involved in nuclear envelope permeability and in chromosome
segregation, has similarity to Nup157p
UDP-N-acetyl-glucosamine-1-P transferase, transfers Glc-Nac-P
from UDP-GlcNac to Dol-P in the ER in the first step of the
dolichol pathway of protein asparagine-linked glycosylation;
inhibited by tunicamycin
Synthetic with Old Yellow Enzyme
endonuclease
Uracil permease, localized to the plasma membrane; expression
is tightly regulated by uracil levels and environmental cues
Translation release factor involved in translation termination;
mutant form acts as a recessive omnipotent suppressor
GPI-anchored protein of unknown function, has a possible role
in apical bud growth; GPI-anchoring on the plasma membrane
crucial to function; similar to Sps2p and Pst1p
protein; rpl19a and rpl19b single null mutations result in slow
growth, while the double null mutation is lethal
Chitin synthase III, catalyzes the transfer of Nacetylglucosamine (GlcNAc) to chitin; required for synthesis of
the majority of cell wall chitin, the chitin ring during bud
emergence, and spore wall chitosan
Essential nucleolar protein, putative DEAD-box RNA helicase
required for maintenance of M1 dsRNA virus; involved in
biogenesis of large (60S) ribosomal subunits
YBL031W
SHE1
YBR172C
SMY2
YBR106W
PHO88
YBR187W
None
YBL061C
SKT5
YBL068W
PRS4
YBR271W
YBR159W
None
None
YBR175W
SWD3
YBR087W
RFC5
YBR263W
SHM1
YPL242C
IQG1
Cytoskeletal protein of unknown function; overexpression
causes growth arrest
partial suppressor of myo2-66; Kinesin-related protein
suppressing myosin defects (MYO2)
Probable membrane protein, involved in phosphate transport;
pho88 pho86 double null mutant exhibits enhanced synthesis of
repressible acid phosphatase at high inorganic phosphate
concentrations
Activator of Chs3p (chitin synthase III), recruits Chs3p to the
bud neck via interaction with Bni4p; has similarity to Shc1p,
which activates Chs3p during sporulation
5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, involved
in nucleotide, histidine, and tryptophan biosynthesis; one of a
five related enzymes, which are active as heteromultimeric
complexes
Subunit of the COMPASS complex, which methylates histone
H3 on lysine 4 and is required in transcriptional silencing near
telomeres
Subunit of heteropentameric Replication factor C (RF-C), which
is a DNA binding protein and ATPase that acts as a clamp
loader of the proliferating cell nuclear antigen (PCNA)
processivity factor for DNA polymerases delta and epsilon
Serine hydroxymethyltransferase, mitochondrial
Essential protein required for determination of budding pattern,
promotes localization of axial markers Bud4p and Cdc12p and
functionally interacts with Sec3p, localizes to the contractile
ring during anaphase, member of the IQGAP family
(56) MODULE 64
YDL064W
UBC9
YGR123C
PPT1
YNL030W
HHF2
YGR123C
PPT1
YPL002C
SNF8
YGR123C
PPT1
(APCC)
derepression
YGR188C
BUB1
checkpoint gene involved in permitting entry into mitosis
depending upon the assembly state of microtubules;
Serine/threonine protein kinase required for cell cycle arrest in
response to loss of microtubule function
Module genes
YCL050C
APA1
YER056C-A
RPL34A
YOR210W
RPB10
YIL018W
RPL2B
YDL082W
RPL13A
YPR043W
RPL43A
YLR029C
RPL15A
YNL067W
RPL9B
YKR059W
TIF1
YGR211W
ZPR1
YGR085C
RPL11B
YHR021C
RPS27B
YAL035W
FUN12
YPL142C
None
YMR142C
RPL13B
YLR198C
None
Diadenosine 5',5''-P1,P4-tetraphosphate phosphorylase I (AP4A
phosphorylase), involved in catabolism of bis(5'-nucleosidyl)
tetraphosphates; has similarity to Apa2p
protein
I, II, and III
Protein component of the large (60S) ribosomal subunit,
identical to Rpl2Ap and has similarity to E. coli L2 and rat L8
ribosomal proteins; expression is upregulated at low
temperatures
identical to Rpl13Bp; not essential for viability; has similarity to
rat L13 ribosomal protein
identical to Rpl43Bp and has similarity to rat L37a ribosomal
protein; null mutation confers a dominant lethal phenotype
protein; binds to 5.8 S rRNA
ribosomal proteins
translation initiation factor eIF4A
Essential protein with two zinc fingers, present in the nucleus of
growing cells but relocates to the cytoplasm in starved cells via
a process mediated by Cpr1p; binds to translation elongation
factor eEF-1 (Tef1p)
identical to Rpl11Ap; involved in ribosomal assembly; depletion
causes degradation of proteins and RNA of the 60S subunit; has
similarity to E. coli L5 and rat L11
Protein component of the small (40S) ribosomal subunit; nearly
identical to Rps27Ap and has similarity to rat S27 ribosomal
protein
GTPase, required for general translation initiation by promoting
Met-tRNAiMet binding to ribosomes and ribosomal subunit
joining; homolog of bacterial IF2
identical to Rpl13Ap; not essential for viability; has similarity to
rat L13 ribosomal protein
YLR340W
RPP0
YDR012W
RPL4B
YDR447C
RPS17B
YOR224C
RPB8
YOR312C
RPL20B
YDL184C
RPL41A
YOR369C
RPS12
YOL121C
RPS19A
YNL265C
IST1
YLR048W
RPS0B
YPL081W
RPS9A
YMR217W
GUA1
YHL001W
RPL14B
YIL052C
RPL34B
YER074W
RPS24A
YER146W
LSM5
YDL130W
RPP1B
Conserved ribosomal protein P0 similar to rat P0, human P0,
and E. coli L10e; shown to be phosphorylated on serine 302
ribosomal proteins
Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly
protein
I, II, and III
identical to Rpl20Ap and has similarity to rat L18a ribosomal
protein
Ribosomal protein L47 of the large (60S) ribosomal subunit,
protein; comprised of only 25 amino acids; rpl41a rpl41b double
null mutant is viable
Protein component of the small (40S) ribosomal subunit; has
similarity to rat ribosomal protein S12
identical to Rps19Bp and has similarity to rat S19 ribosomal
protein
Putative translation initiation factor, as suggested by
computational analysis of large-scale protein-protein interaction
data
Protein component of the small (40S) ribosomal subunit, nearly
identical to Rps0Ap; required for maturation of 18S rRNA along
with Rps0Ap; deletion of either RPS0 gene reduces growth rate,
deletion of both genes is lethal
identical to Rps9Ap and has similarity to E. coli S4 and rat S9
ribosomal proteins
GMP synthase, an enzyme that catalyzes the second step in the
biosynthesis of GMP from inosine 5'-phosphate (IMP);
transcription is not subject to regulation by guanine but is
negatively regulated by nutrient starvation
identical to Rpl14Ap and has similarity to rat L14 ribosomal
protein
protein
Protein component of the small (40S) ribosomal subunit;
protein
Component of small nuclear ribonucleoprotein complexes
involved in RNA processing, splicing, and decay
Ribosomal protein P1 beta, a component of the ribosomal stalk,
which is involved in the interaction between translational
elongation factors and the ribosome; accumulation of P1 in the
cytoplasm is regulated by phosphorylation and interaction with
the P2 stalk component
YDL228C
YOR277C
YNL149C
YGR109C
None
None
None
CLB6
YBR181C
RPS6B
YAL003W
EFB1
YLR406C
RPL31B
YGL102C
None
YLR197W
SIK1
YPL263C
KEL3
YKL181W
PRS1
YPL198W
RPL7B
YML022W
APT1
YML056C
IMD4
YDR382W
RPP2B
YOR169C
None
YDL191W
RPL35A
YBR031W
RPL4A
YGR160W
None
YLR249W
YEF3
role in DNA replication during S phase; B-type cyclin
protein
Translation elongation factor 1 beta; stimulates nucleotide
exchange to regenerate EF-1 alpha-GTP for the next elongation
cycle; part of the EF-1 complex, which facilitates binding of
aminoacyl-tRNA to the ribosomal A site
protein; associates with the karyopherin Sxm1p
Component of the small (ribosomal) subunit (SSU)
processosome that contains U3 snoRNA; similar to microtubule
binding proteins
Cytoplasmic protein of unknown function
complexes
ribosomal proteins; contains a conserved C-terminal Nucleic
acid Binding Domain (NDB2)
Adenine phosphoribosyltransferase, catalyzes the formation of
AMP from adenine and 5-phosphoribosylpyrophosphate;
involved in the salvage pathway of purine nucleotide
biosynthesis
Inosine monophosphate dehydrogenase, catalyzes the first step
of GMP biosynthesis, member of a four-gene family in S.
cerevisiae, constitutively expressed
Ribosomal protein P2 beta, a component of the ribosomal stalk,
elongation factors and the ribosome; regulates the accumulation
of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm
protein
N-terminally acetylated protein component of the large (60S)
ribosomal subunit, nearly identical to Rpl4Bp and has similarity
to E. coli L4 and rat L4 ribosomal proteins
stimulates the binding of aminoacyl-tRNA (AA-tRNA) to
ribosomes by releasing EF-1 alpha from the ribosomal complex;
contains two ABC cassettes, and binds and hydrolyses ATP; EF3 (translational elongation factor 3)
YLR185W
RPL37A
YKL081W
TEF4
YDR025W
RPS11A
YHL011C
PRS3
YGL147C
RPL9A
YDR091C
RLI1
YMR194W
RPL36A
YJR124C
None
YDR418W
RPL12B
YDR450W
RPS18A
YER042W
MXR1
YOR309C
None
YNL301C
RPL18B
YIL069C
RPS24B
YOR276W
CAF20
YPR132W
RPS23B
YLR062C
BUD28
YJL190C
RPS22A
similarity to Rpl37Bp and to rat L37 ribosomal protein
Translation elongation factor EF-1gamma
identical to Rps11Bp and has similarity to E. coli S17 and rat
S11 ribosomal proteins
complexes
identical to Rpl9Bp and has similarity to E. coli L6 and rat L9
ribosomal proteins
Protein with strong similarity to human RNase L Inhibitor
(RLI), required for vegetative growth and early sporulation;
putative member of nontransporter group of ATP-binding
cassette (ABC) superfamily
ribosomal subunit, nearly identical to Rpl36Ap and has
similarity to rat L36 ribosomal protein; binds to 5.8 S rRNA
identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow
growth and slow translation; has similarity to E. coli L11 and rat
L12 ribosomal proteins
peptide Methionine sulfoXide Reductase 1; peptide methionine
sulfoxide reductase
protein
protein
binds to eIF-4E, the mRNA cap-binding protein, and represses
cap-dependent translation initiation by interfering with the
interaction of eIF4E and eIF4G; mRNA cap-binding protein
(eIF4F) 20K subunit
Ribosomal protein 28 (rp28) of the small (40S) ribosomal
subunit, required for translational accuracy; nearly identical to
Rps23Ap and similar to E. coli S12 and rat S23 ribosomal
proteins; deletion of both RPS23A and RPS23B is lethal
ORF overlaps the verified gene RPL22A; diploid mutant
displays a weak budding pattern phenotype in a systematic assay
YJL189W
RPL39
YBL087C
RPL23A
YER102W
RPS8B
YJR063W
RPA12
YML063W
RPS1B
YBR025C
None
YOR096W
RPS7A
YOR168W
GLN4
YOR272W
YJL138C
YTM1
TIF2
YBR048W
RPS11B
YJL177W
RPL17B
YGR265W
None
YER036C
ARB1
YJR123W
RPS5
YIL133C
RPL16A
YDR395W
SXM1
YDL051W
LHP1
S15a ribosomal proteins
similarity to rat L39 ribosomal protein; required for ribosome
biogenesis; exhibits genetic interactions with SIS1 and PAB1
identical to Rpl23Bp and has similarity to E. coli L14 and rat
protein
RNA polymerase I subunit A12.2; contains two zinc binding
domains, and the N terminal domain is responsible for anchoring
to the RNA pol I complex
Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly
identical to Rps1Ap and has similarity to rat S3a ribosomal
protein
identical to Rps7Bp; interacts with Kti11p; deletion causes
hypersensitivity to zymocin; has similarity to rat S7 and
Xenopus S8 ribosomal proteins
Glutamine tRNA synthetase, monomeric class I tRNA
synthetase that catalyzes the specific glutaminylation of
tRNA(Glu); N-terminal domain proposed to be involved in
enzyme-tRNA interactions
microtubule-associated protein
translation initiation factor eIF4A
identical to Rps11Ap and has similarity to E. coli S17 and rat
identical to Rpl17Ap and has similarity to E. coli L22 and rat
ATPase of the ATP-binding cassette (ABC) family involved in
ribosome biogenesis, has similarity to Gcn20p
Protein component of the small (40S) ribosomal subunit, the
least basic of the non-acidic ribosomal proteins; phosphorylated
in vivo; essential for viability; has similarity to E. coli S7 and rat
ribosomal subunit, binds to 5.8 S rRNA; has similarity to
Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins;
transcriptionally regulated by Rap1p
Nuclear protein; has similarity to Cse1p homologs including
Nmd5p, Cse1p, Lph2p, and the human cellular apoptosis
susceptibility protein, CAS1; also has similarity to the
karyopherin Kap95p
RNA binding protein required for maturation of tRNA and
snRNA precursors; acts as a molecular chaperone for RNAs
transcribed by polymerase III; homologous to human La (SS-B)
autoantigen
YDL157C
None
YPL249C-A
RPL36B
YKR094C
RPL40B
YIL148W
RPL40A
YLR061W
RPL22A
YGL031C
RPL24A
YBR189W
RPS9B
YBL039C
URA7
YMR230W
RPS10B
YJR145C
RPS4A
YML073C
RPL6A
YDR471W
RPL27B
YDL081C
RPP1A
YLR017W
MEU1
YOL139C
CDC33
Fusion protein, identical to Rpl40Ap, that is cleaved to yield
ubiquitin and a ribosomal protein of the large (60S) ribosomal
subunit with similarity to rat L40; ubiquitin may facilitate
assembly of the ribosomal protein into ribosomes
Fusion protein, identical to Rpl40Bp, that is cleaved to yield
ubiquitin and a ribosomal protein of the large (60S) ribosomal
subunit with similarity to rat L40; ubiquitin may facilitate
assembly of the ribosomal protein into ribosomes
similarity to Rpl22Bp and to rat L22 ribosomal protein
nearly identical to Rpl24Bp and has similarity to rat L24
ribosomal protein; not essential for translation but may be
required for normal translation rate
identical to Rps9Bp and has similarity to E. coli S4 and rat S9
ribosomal proteins
CTP synthase, catalyzes the ATP-dependent transfer of amide
nitrogen from glutamine to UTP to form CTP in last step of
pyrimidine biosynthesis, very similar to URA8p but appears to
be responsible for the majority of CTP synthesis
identical to Rps10Ap and has similarity to rat ribosomal protein
S10
mutation affects 20S pre-rRNA processing; identical to Rps4Bp
and has similarity to rat S4 ribosomal protein
ribosomal subunit, has similarity to Rpl6Bp and to rat L6
ribosomal protein; binds to 5.8S rRNA
protein
Ribosomal protein P1 alpha, a component of the ribosomal stalk,
elongation factors and the ribosome; accumulation of P1 in the
cytoplasm is regulated by phosphorylation and interaction with
the P2 stalk component
Methylthioadenosine phosphorylase (MTAP), catalyzes the
initial step in the methionine salvage pathway; affects polyamine
biosynthesis through regulation of ornithine decarboxylase
(Spe1p) activity; regulates ADH2 gene expression
Cytoplasmic mRNA cap binding protein; the eIF4E-cap
complex is responsible for mediating cap-dependent mRNA
translation via interactions with the translation initiation factor
eIF4G (Tif4631p or Tif4632p)
YHR203C
RPS4B
YLR186W
EMG1
YMR260C
TIF11
YGL076C
RPL7A
YDR500C
RPL37B
YOR021C
None
YER131W
RPS26B
YDL061C
RPS29B
YPR102C
RPL11A
YOR182C
RPS30B
YNL302C
RPS19B
YEL054C
RPL12A
YOR293W
RPS10A
YGR159C
NSR1
YGL030W
RPL30
YPL079W
RPL21B
YHL015W
RPS20
protein
Protein required for the maturation of the 18S rRNA and for 40S
ribosome production; associated with spindle/microtubules;
nuclear localization depends on physical interaction with
Nop14p; may bind snoRNAs
Translation initiation factor eIF1A
ribosomal proteins; contains a conserved C-terminal Nucleic
acid Binding Domain (NDB2)
similarity to Rpl37Ap and to rat L37 ribosomal protein
protein
identical to Rps29Ap and has similarity to rat S29 and E. coli
identical to Rpl11Bp; involved in ribosomal assembly; depletion
causes degradation of proteins and RNA of the 60S subunit; has
similarity to E. coli L5 and rat L11
protein
protein
identical to Rpl12Bp; rpl12a rpl12b double mutant exhibits slow
growth and slow translation; has similarity to E. coli L11 and rat
identical to Rps10Bp and has similarity to rat ribosomal protein
S10
Nucleolar protein that binds nuclear localization sequences,
required for pre-rRNA processing and ribosome biogenesis
similarity to rat L30 ribosomal protein; involved in pre-rRNA
processing in the nucleolus; autoregulates splicing of its
transcript
protein
overproduction suppresses mutations affecting RNA polymerase
III-dependent transcription; has similarity to E. coli S10 and rat
YOR234C
RPL33B
YDL136W
RPL35B
YFR032C-A
RPL29
YMR116C
ASC1
YJL098W
SAP185
YDR002W
YRB1
YPL197C
None
YDR429C
TIF35
YGL189C
RPS26A
YOR214C
None
YNL141W
AAH1
YNL255C
GIS2
YCR031C
RPS14A
YFR031C-A
RPL2A
YLR150W
STM1
YKL006W
RPL14A
YKL056C
None
YGL120C
PRP43
YBL072C
RPS8A
YLR367W
RPS22B
nearly identical to Rpl33Ap and has similarity to rat L35a;
rpl33b null mutant exhibits normal growth while rpl33a rpl33b
double null mutant is inviable
protein
similarity to rat L29 ribosomal protein; not essential for
translation, but required for proper joining of the large and small
ribosomal subunits and for normal translation rate
WD repeat protein (G-beta like protein) that interacts with the
translational machinery; G-beta like protein
Yeast Ran Binder #1; suppressor of FUS1; homolog of mouse
HTF9a and human RanBP1; nuclear GTPase-activating protein
for Ran
Subunit of the core complex of translation initiation factor
3(eIF3), which is essential for translation
protein
Adenine deaminase (adenine aminohydrolase), involved in
purine salvage and nitrogen catabolism
Putative zinc finger protein with similarity to human CNBP,
proposed to be involved in the RAS/cAMP signaling pathway
subunit, required for ribosome assembly; mutations confer
resistance to cryptopleurine; nearly identical to Rps14Bp and
similar to E. coli S11 and rat S14 ribosomal proteins
ribosomal proteins
ribosomal subunit, nearly identical to Rpl14Bp and has
similarity to rat L14 ribosomal protein; rpl14a csh5 double null
mutant exhibits synthetic slow growth
RNA helicase in the DEAH-box family, involved in release of
the lariat-intron from the spliceosome
protein
YPL143W
RPL33A
YHL033C
RPL8A
YDR417C
None
YGL135W
RPL1B
YML024W
RPS17A
YJR094W-A
RPL43B
YGR027C
RPS25A
YNL178W
RPS3
YLR076C
None
YHR010W
RPL27A
YJL188C
BUD19
YPL131W
RPL5
YPL211W
NIP7
YLL045C
RPL8B
YGL123W
RPS2
YJR070C
LIA1
YOR167C
RPS28A
S15a ribosomal proteins
N-terminally acetylated ribosomal protein L37 of the large (60S)
ribosomal subunit, nearly identical to Rpl33Bp and has
similarity to rat L35a; rpl33a null mutant exhibits slow growth
while rpl33a rpl33b double null mutant is inviable
nearly identical to Rpl8Bp and has similarity to rat L7a
ribosomal protein; mutation results in decreased amounts of free
60S subunits
to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double
null mutation is lethal
Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly
protein
identical to Rpl43Ap and has similarity to rat L37a ribosomal
protein
protein
Protein component of the small (40S) ribosomal subunit, has
apurinic/apyrimidinic (AP) endonuclease activity; essential for
viability; has similarity to E. coli S3 and rat S3 ribosomal
proteins
protein
ORF overlaps the verified gene RPL39; diploid mutant displays
a weak budding pattern phenotype in a systematic assay
Protein component of the large (60S) ribosomal subunit with
similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S
rRNA and is required for 60S subunit assembly
Nip7p is required for 60S ribosome subunit biogenesis; involved
in ribosome biogenesis
nearly identical to Rpl8Ap and has similarity to rat L7a
ribosomal protein; mutation results in decreased amounts of free
60S subunits
Protein component of the small (40S) subunit, essential for
control of translational accuracy; has similarity to E. coli S5 and
rat S2 ribosomal proteins
Protein that binds to the C-terminal domain of Hyp2p (eIF5A);
has four to five HEAT-like repeats
YOR095C
RKI1
YEL055C
POL5
YDL229W
SSB1
YPR118W
None
YGR118W
RPS23A
YGR214W
RPS0A
YDL133C-A
RPL41B
YLR167W
RPS31
YHR127W
None
YHR089C
GAR1
YCR087W
None
YGL103W
RPL28
YML026C
RPS18B
YNL162W
RPL42A
YGR148C
RPL24B
YGR034W
RPL26B
YLR388W
RPS29A
protein
Ribose-5-phosphate ketol-isomerase
Protein with sequence similarity to the human MybBP1A and
weak sequence similar to B-type DNA polymerases, not
required for chromosomal DNA replication; required for the
synthesis of rRNA
Stress-Seventy Subfamily B; involved in translation, perhaps by
guiding the nascent chain through the ribosome; cytoplasmic
member of the HSP70 family
subunit, required for translational accuracy; nearly identical to
Rps23Bp and similar to E. coli S12 and rat S23 ribosomal
proteins; deletion of both RPS23A and RPS23B is lethal
identical to Rps0Bp; required for maturation of 18S rRNA along
with Rps0Bp; deletion of either RPS0 gene reduces growth rate,
deletion of both genes is lethal
protein; comprised of only 25 amino acids; rpl41a rpl41b double
null mutant is viable
Fusion protein that is cleaved to yield a ribosomal protein of the
small (40S) subunit and ubiquitin; ubiquitin may facilitate
assembly of the ribosomal protein into ribosomes; interacts
genetically with translation factor eIF2B
Protein component of the H/ACA snoRNP pseudouridylase
complex, involved in the modification and cleavage of the 18S
pre-rRNA
Ribosomal protein L29 of the large (60S) ribosomal subunit, has
similarity to E. coli L15 and rat L27a ribosomal proteins; may
have peptidyl transferase activity; can mutate to cycloheximide
resistance
protein
nearly identical to Rpl24Ap and has similarity to rat L24
ribosomal protein; not essential for translation but may be
required for normal translation rate
L26 ribosomal proteins; binds to 5.8S rRNA
identical to Rps29Bp and has similarity to rat S29 and E. coli
YLL044W
None
YDR454C
GUK1
YOL120C
RPL18A
YOL040C
RPS15
YNL096C
RPS7B
YJL136C
RPS21B
YLR441C
RPS1A
YMR121C
RPL15B
YOL127W
RPL25
YOL039W
RPP2A
YJL183W
MNN11
YJL191W
RPS14B
YLR448W
RPL6B
YDR064W
RPS13
YDL083C
RPS16B
YDL201W
TRM8
Guanylate kinase, converts GMP to GDP; required for growth
and mannose outer chain elongation of cell wall N-linked
glycoproteins
protein; intron of RPL18A pre-mRNA forms stem-loop
structures that are a target for Rnt1p cleavage leading to
degradation
similarity to E. coli S19 and rat S15 ribosomal proteins
identical to Rps7Ap; interacts with Kti11p; deletion causes
hypersensitivity to zymocin; has similarity to rat S7 and
Xenopus S8 ribosomal proteins
protein
Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly
identical to Rps1Bp and has similarity to rat S3a ribosomal
protein
Protein compoent of the large (60S) ribosomal subunit, has
similarity to E. coli L23 and rat L23a ribosomal proteins; binds
to 26S rRNA via a conserved C-terminal motif
Ribosomal protein P2 alpha, a component of the ribosomal stalk,
elongation factors and the ribosome; regulates the accumulation
of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm
Subunit of a Golgi mannosyltransferase complex that also
contains Anp1p, Mnn9p, Mnn10p, and Hoc1p, and mediates
elongation of the polysaccharide mannan backbone; has
homology to Mnn10p
subunit, required for ribosome assembly; mutations confer
resistance to cryptopleurine; nearly identical to Rps14Ap and
similar to E. coli S11 and rat S14 ribosomal proteins
similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to
5.8S rRNA
similarity to E. coli S15 and rat S13 ribosomal proteins
identical to Rps16Ap and has similarity to E. coli S9 and rat S16
ribosomal proteins
Subunit of a tRNA methyltransferase complex composed of
Trm8p and Trm82p that catalyzes 7-methylguanosine
modification of tRNA
YPR044C
YNL244C
None
SUI1
YEL042W
GDA1
YEL026W
SNU13
YLR333C
RPS25B
YLR325C
RPL38
YOL077C
BRX1
YHR141C
RPL42B
YPL220W
RPL1A
YPL238C
None
YLR372W
SUR4
YLR287C-A
RPS30A
YKL180W
RPL17A
YKL156W
RPS27A
YHR068W
DYS1
YBL092W
RPL32
YER117W
RPL23B
YDL151C
BUD30
translation initiation factor eIF1
Guanosine diphosphatase located in the Golgi, involved in the
transport of GDP-mannose into the Golgi lumen by converting
GDP to GMP after mannose is transferred its substrate
U3 snoRNA); RNA binding protein (putative), similar to
Nhp2p; U4/U6.U5 snRNP component
protein
similarity to rat L38 ribosomal protein
Nucleolar protein involved in the biogenesis of large ribosomal
subunits; depletion leads to defects in rRNA processing and a
block in the assembly of large ribosomal subunits; possesses a
sigma(70)-like RNA-binding motif
identical to Rpl42Ap and has similarity to rat L44; required for
propagation of the killer toxin-encoding M1 double-stranded
RNA satellite of the L-A double-stranded RNA virus
to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double
null mutation is lethal
Elongase III synthesizes 20-26-carbon fatty acids from C18CoA primers; involved in fatty acid biosynthesis
protein
L17 ribosomal proteins; copurifies with the components of the
outer kinetochore DASH complex
protein
Deoxyhypusine synthase, catalyzes formation of deoxyhypusine,
the first step in hypusine biosynthesis; triggers posttranslational
hypusination of translation elongation factor eIF-5A and
regulates its intracellular levels; tetrameric
similairty to rat L32 ribosomal protein; overexpression disrupts
telomeric silencing
ORF overlaps the verified gene RPC53; diploid mutant displays
YNL064C
YDJ1
YBR191W
RPL21A
YLR344W
RPL26A
YLR264W
RPS28B
YPL090C
RPS6A
YMR242C
RPL20A
YLR432W
IMD3
YHR128W
FUR1
(57) MODULE 65
YPR013C
None
YOR363C
PIP2
YNL305C
None
YDR195W
REF2
a weak budding pattern phenotype in a systematic assay
yeast dnaJ homolog (nuclear envelope protein); heat shock
protein
protein
L26 ribosomal proteins; binds to 5.8S rRNA
protein
protein
identical to Rpl20Bp and has similarity to rat L18a ribosomal
protein
Inosine monophosphate dehydrogenase, catalyzes the first step
of GMP biosynthesis, member of a four-gene family in S.
cerevisiae, constitutively expressed
Uracil phosphoribosyltransferase, synthesizes UMP from uracil;
involved in the pyrimidine salvage pathway
peroxisome induction pathway 2 (PIP2); transcriptional activator
of peroxisome proliferation; may form heterodimer with Oaf1 to
activate oleate-inducible gene expression; activator of
peroxisome proliferation
snoRNA maturation
Genotype regulators
YVH1(2,4) DAL1(2,2) DAL4(2,2) DAL2(1,4) DCG1(3,3)
YIR030W-A DAL7(1,2) DAL3(2,4) MGA2(15,4) LYS1(0,1)
YIR035C YIR036C YIR036W-A HYR1(0,3) GTT1(1,20)
M9_415311_420076
Module genes
YJL077C
YDR259C
ICS3
YAP6
YHL035C
VMR1
YDR263C
DIN7
YIR019C
MUC1
Protein of unknown function, member of the ATP-binding
cassette (ABC) family, potential Cdc28p substrate
Mitochondrial nuclease functioning in DNA repair and
replication, modulates the stability of the mitochondrial genome,
induced by exposure to mutagens, also induced during meiosis
at a time nearly coincident with commitment to recombination
GPI-anchored cell surface glycoprotein required for diploid
pseudohyphal formation and haploid invasive growth,
transcriptionally regulated by the MAPK pathway (via Ste12p
and Tec1p) and the cAMP pathway (via Flo8p)
YHL042W
YPL236C
YHL043W
None
None
ECM34
YDL037C
BSC1
YKL202W
YDL038C
YKL200C
YOR009W
None
None
None
TIR4
YNL142W
MEP2
YDL039C
PRM7
Protein of unconfirmed function, similar to cell surface flocculin
Muc1p; ORF exhibits genomic organization compatible with a
translational readthrough-dependent mode of expression
None
Ammonia permease; belongs to a ubiquitous family of
cytoplasmic membrane proteins that transport only ammonium
(NH4+)
Pheromone-regulated protein, predicted to have one
transmembrane segment; promoter contains Gcn4p binding
elements
(58) MODULE 67
Genotype regulators
YDR034C-A YDR034W-B ARO3(0,3) EHD3(0,3) KRS1(0,3)
ENA5(29,341) ENA2(24,290) ENA1(13,15)
M4_527445_527517
Module genes
YDR038C
ENA5
YDR033W
MRH1
YDR039C
ENA2
YDR040C
ENA1
YCR073C
SSK22
Protein with similarity to P-type ATPase sodium pumps
Protein that localizes primarily to the plasma membrane, also
found at the nuclear envelope; has similarity to Hsp30p and
Yro2p, which are induced during heat shock
P-type ATPase sodium pump, involved in Na+ efflux to allow
salt tolerance; likely not involved in Li+ efflux
P-type ATPase sodium pump, involved in Na+ and Li+ efflux to
allow salt tolerance
functionally redundant with, and homologous to, SSK2; protein
kinase
(59) MODULE 68
YOR047C
STD1
YDL170W
UGA3
YOR047C
STD1
YNL068C
FKH2
YBR212W
NGR1
YJL056C
ZAP1
silencing at HML and HMR; potential Cdc28p substrate
YMR019W
Module genes
STB4
YOR099W
KTR1
YOL076W
MDM20
YNL169C
PSD1
YJL153C
INO1
YHR177W
YJR106W
None
ECM27
YOL013C
HRD1
YKL073W
LHS1
YCL043C
PDI1
YPL021W
ECM23
YDR516C
EMI2
YLR133W
YMR214W
YGL126W
CKI1
SCJ1
SCS3
YJR073C
OPI3
YDR519W
FPR2
zinc-finger domains
Alpha-1,2-mannosyltransferase involved in O- and N-linked
protein glycosylation; member of the KRE2/MNT1
mannosyltransferase family
Subunit of the NatB N-terminal acetyltransferase, which
catalyzes acetylation of the amino-terminal methionine residues
of all proteins beginning with Met-Asp or Met-Glu and of some
proteins beginning with Met-Asn or Met-Met; involved in
mitochondrial inheritance and actin assembly
Phosphatidylserine decarboxylase of the mitochondrial inner
membrane, converts phosphatidylserine to
phosphatidylethanolamine
Inositol 1-phosphate synthase, involved in synthesis of inositol
phosphates and inositol-containing phospholipids; transcription
is coregulated with other phospholipid biosynthetic genes by
Ino2p and Ino4p, which bind the UASINO DNA element
Ubiquitin-protein ligase required for endoplasmic reticulumassociated degradation (ERAD) of misfolded proteins;
genetically linked to the unfolded protein response (UPR);
regulated through association with Hrd3p; contains an H2 ring
finger
Molecular chaperone of the endoplasmic reticulum lumen,
involved in polypeptide translocation and folding; member of
the Hsp70 family; localizes to the lumen of the ER; regulated by
the unfolded protein response pathway
Protein disulfide isomerase, multifunctional protein resident in
the endoplasmic reticulum lumen, essential for the formation of
disulfide bonds in secretory and cell-surface proteins,
unscrambles non-native disulfide bonds
Non-essential protein of unconfirmed function; affects prerRNA processing, may act as a negative regulator of the
transcription of genes involved in pseudohyphal growth;
homologous to Srd1p
Non-essential protein of unknown function required for
transcriptional induction of the early meiotic-specific
transcription factor IME1, also required for sporulation
choline kinase
dnaJ homolog
Protein required for inositol prototrophy
Phospholipid methyltransferase (methylene-fatty-acylphospholipid synthase), catalyzes the last two steps in
phosphatidylcholine biosynthesis
Membrane-bound peptidyl-prolyl cis-trans isomerase (PPIase),
binds to the drugs FK506 and rapamycin; expression pattern
suggests possible involvement in ER protein trafficking
YKL126W
YPK1
YHR142W
CHS7
YDR277C
MTH1
YML028W
TSA1
YOL031C
SIL1
YBR201W
DER1
YDL193W
None
YGR284C
ERV29
YJL082W
IML2
YMR184W
None
YML130C
ERO1
YNL043C
YNL170W
None
None
YJL034W
KAR2
YKL165C
MCD4
YER142C
MAG1
YOR288C
MPD1
YLL016W
YKR011C
YNL144C
(60) MODULE 69
None
None
None
Protein of unknown function, involved in chitin biosynthesis by
regulating Chs3p export from the ER
Thioredoxin-peroxidase (TPx), reduces H2O2 and alkyl
hydroperoxides with the use of hydrogens provided by
thioredoxin, thioredoxin reductase, and NADPH; provides
protection against oxidation systems that generate reactive
oxygen and sulfur species
ER-localized protein required for protein translocation into the
ER, interacts with the ATPase domain of the Kar2p chaperone
suggesting some role in modulating its activity; homolog of
Yarrowia lipolytica SLS1; GrpE-like protein in the ER
Endoplasmic reticulum membrane protein, required for the
protein degradation process associated with the ER, involved in
the retrograde transport of misfolded or unassembled proteins
Protein localized to COPII-coated vesicles, involved in vesicle
formation and incorporation of specific secretory cargo
Protein of unknown function, green fluorescent protein (GFP)fusion protein localizes to the cytoplasm and nucleus
Glycoprotein required for oxidative protein folding in the
endoplasmic reticulum
ATPase involved in protein import into the ER, also acts as a
chaperone to mediate protein folding in the ER and may play a
role in ER export of soluble proteins; regulates the unfolded
protein response via interaction with Ire1p
Protein involved in glycosylphosphatidylinositol (GPI) anchor
synthesis; multimembrane-spanning protein that localizes to the
endoplasmic reticulum; highly conserved among eukaryotes
3-methyl-adenine DNA glycosylase involved in protecting DNA
against alkylating agents; initiates base excision repair by
removing damaged bases to create abasic sites that are
subsequently repaired
Member of the protein disulfide isomerase (PDI) family;
overexpression suppresses the defect in maturation of
carboxypeptidase Y, and defects in other essential Pdi1p
functions, caused by PDI1 deletion
YLR452C
SST2
YGR097W
ASK10
YCL055W
KAR4
YDR195W
REF2
YDR283C
GCN2
YPR070W
MED1
Module genes
YML048W-A
YPR115W
None
None
YHR005C
GPA1
YJL157C
FAR1
YBR083W
TEC1
YKL189W
HYM1
YML046W
PRP39
YBL016W
FUS3
YMR065W
KAR5
YNL192W
CHS1
Protein involved in desensitization to alpha-factor pheromone;
member of the RGS (regulator of G-protein signalling) family;
GTPase-activating protein
snoRNA maturation
regulation
and alpha cells
Cyclin-dependent kinase inhibitor that mediates cell cycle arrest
in response to pheromone; also forms a complex with Cdc24p,
Ste4p, and Ste18p that may specify the direction of polarized
growth during mating; potential Cdc28p substrate
transcription factor of the TEA/ATTS DNA-binding domain
family, regulator of Ty1 expression
Component of the RAM signaling network that is involved in
regulation of Ace2p activity and cellular morphogenesis,
interacts with Kic1p and Sog2p, localizes to sites of polarized
growth during budding and during the mating response
U1 snRNP protein involved in splicing, contains multiple
tetriatricopeptide repeats
Mitogen-activated protein kinase (MAPK) involved in mating
pheromone response; activated by phosporylation by Ste7p;
controls different aspects of the mating response by
phosphorylating transcriptional and cytoplasmic targets
Protein required for nuclear membrane fusion during
karyogamy, localizes to the membrane with a soluble portion in
the endoplasmic reticulum lumen, may form a complex with
Jem1p and Kar2p; expression of the gene is regulated by
pheromone
Chitin synthase I, requires activation from zymogenic form in
order to catalyze the transfer of N-acetylglucosamine (GlcNAc)
to chitin; required for repairing the chitin septum during
cytokinesis; transcription activated by mating factor
YCR089W
FIG2
YDL127W
PCL2
YIL037C
PRM2
YIL117C
PRM5
YBR040W
FIG1
YCL027W
FUS1
YFR026C
YDL089W
None
None
YDR309C
GIC2
YDR085C
AFR1
YNR044W
AGA1
YOR343C
None
YKL104C
GFA1
YJR153W
YDR125C
PGU1
ECM18
YNL279W
PRM1
YMR232W
FUS2
YDR282C
None
YNL042W
BOP3
YKR042W
UTH1
YHR084W
STE12
Cell wall adhesin, expressed specifically during mating; may be
involved in maintenance of cell wall integrity during mating
G1 cyclin, associates with Pho85p cyclin-dependent kinase
(Cdk) to contribute to entry into the mitotic cell cycle, essential
for cell morphogenesis; localizes to sites of polarized cell
growth
Pheromone-regulated protein, predicted to have 4
transmembrane segments and a coiled coil domain; regulated by
Ste12p
Pheromone-regulated protein, predicted to have 1
transmembrane segment; induced during cell integrity signalling
Integral membrane protein required for efficient mating; may
participate in or regulate the low affinity Ca2+ influx system,
which affects intracellular signaling and cell-cell fusion during
mating
Membrane protein localized to the shmoo tip, required for cell
fusion; expression regulated by mating pheromone; proposed to
coordinate signaling, fusion, and polarization events required for
fusion; potential Cdc28p substrate
Protein of unknown function involved in initiation of budding
and cellular polarization, interacts with Cdc42p via the
Cdc42/Rac-interactive binding (CRIB) domain
coordinates regulation of alpha-factor receptor signalling and
induction of morphogenesis during conjugation; cytoskeletal
protein, similar to arrestins
Anchorage subunit of a-agglutinin of a-cells, highly Oglycosylated protein with N-terminal secretion signal and Cterminal signal for addition of GPI anchor to cell wall, linked to
adhesion subunit Aga2p via two disulfide bonds
Glutamine-fructose-6-phosphate amidotransferase, catalyzes the
formation of glucosamine-6-P and glutamate from fructose-6-P
and glutamine in the first step of chitin biosynthesis
Endo-polygalacturonase
Protein of unknown function, similar to Rlp24p
Pheromone-regulated multispanning membrane protein involved
in membrane fusion during mating; predicted to have 5
transmembrane segments and a coiled coil domain; localizes to
the shmoo tip; regulated by Ste12p
Cytoplasmic protein localized to the shmoo tip; required for the
alignment of parental nuclei before nuclear fusion during mating
Protein of unknown function, potential Cdc28p substrate;
overproduction suppresses a pam1 slv3 double null mutation
Youth, involved in determining yeast longevity; involved in cell
growth
Transcription factor that is activated by a MAP kinase signaling
cascade, activates genes involved in mating or
pseudohyphal/invasive growth pathways; cooperates with Tec1p
transcription factor to regulate genes specific for invasive
growth
YDR124W
(61) MODULE 70
YDR496C
YMR019W
None
PUF6
STB4
YDR264C
AKR1
Genotype regulators
CTR9(13,2) PSF3(1,1) PEX11(0,1) SPT20(4,15) DCP1(0,4)
YOL150C GRE2(6,81) FRE7(38,11) YOL153C ZPS1(3,8)
YOL155C YOL155W-A HXT11(6,53) YOL157C ENB1(5,8)
YOL159C YOL159C-A YOL160W YOL161C YOL162W
YOL163W YOL164W YOL164W-A AAD15(7,561) YOL166C
YOL166W-A
M15_1152_43217
Module genes
YAR066W
YIL169C
YOL155C
YAR068W
YHR214W
YHR214W-A
(62) MODULE 71
None
None
None
None
None
None
YJL089W
SIP4
YDR043C
NRG1
YGR288W
MAL13
YCL026C-A
FRM2
YKR099W
BAS1
YGL180W
ATG1
YAL056W
GPB2
transcription
Proposed beta subunit of the heterotrimeric G protein that
interacts with the receptor Grp1p, has signaling role in response
to nutrients; involved in regulation of pseudohyphal growth
through cAMP levels; homolog of Gpb1p
Module genes
YGL249W
ZIP2
YJR154W
None
YMR126C
DLT1
YGR161C
YGR065C
RTS3
VHT1
YNR058W
BIO3
YMR271C
URA10
YIR005W
IST3
YHR199C
FMP34
YGL183C
YER184C
MND1
None
YOR100C
CRC1
YNL125C
ESBP6
YPR078C
None
YNR056C
BIO5
YBR105C
VID24
YGR154C
YPL264C
YLL056C
YIL166C
YJL037W
None
None
None
None
None
YNR057C
BIO4
YJR025C
BNA1
YLL055W
YER065C
None
ICL1
Required for 'ZIPpering' up meiotic chromosomes during
chromosome synapsis; involved in meiotic recombination and
disjunction
Protein of unknown function, deletion causes sensitivity to
thermal stress
Hypothetical ORF
vitamin H transporter; H+-biotin symporter
7,8-diamino-pelargonic acid aminotransferase (DAPA),
catalyzes the second step in the biotin biosynthesis pathway;
BIO3 is in a cluster of 3 genes (BIO3, BIO4, and BIO5) that
mediate biotin synthesis
Fifth step in pyrimidine bio5; Orotate phosphoribosyltransferase
2
Component of the U2 snRNP, required for the first catalytic step
of splicing and for spliceosomal assembly; interacts with Rds3p
and is required for Mer1p-activated splicing
mitochondria
needed for Meiotic Nuclear Divisions
Mitochondrial inner membrane carnitine transporter, required
for carnitine-dependent transport of acetyl-CoA from
peroxisomes to mitochondria during fatty acid beta-oxidation
Protein with similarity to monocarboxylate permeases, appears
not to be involved in transport of monocarboxylates such as
lactate, pyruvate or acetate across the plasma membrane
Putative transmembrane protein involved in the biotin
biosynthesis pathway; responsible for uptake of 7-keto 8aminopelargonic acid; BIO5 is in a cluster of 3 genes (BIO3,
BIO4, and BIO5) that mediate biotin synthesis
also involved in vacuolar protein targeting; peripheral vesicle
membrane protein
Dethiobiotin synthetase, catalyzes the third step in the biotin
biosynthesis pathway; BIO4 is in a cluster of 3 genes (BIO3,
BIO4, and BIO5) that mediate biotin synthesis; expression
appears to be repressed at low iron levels
3-hydroxyanthranilic acid dioxygenase, required for
biosynthesis of nicotinic acid from tryptophan via kynurenine
pathway
Isocitrate lyase, catalyzes the formation of succinate and
YDL101C
DUN1
YNL183C
NPR1
YBR294W
SUL1
YCL049C
None
YDL234C
GYP7
YHL036W
MUP3
YDL214C
PRR2
YJR149W
YLR152C
YHR112C
None
None
None
YIR017C
MET28
YMR306C-A
YER185W
None
None
YDR076W
RAD55
YGR110W
None
YNR050C
LYS9
YDR186C
YOR292C
YGR197C
None
None
SNG1
YDL215C
GDH2
YIR042C
(63) MODULE 72
Genotype regulators
None
M4_85846_106892
glyoxylate from isocitrate, a key reaction of the glyoxylate
cycle; expression of ICL1 is induced by growth on ethanol and
repressed by growth on glucose
repair
Protein kinase that stabilizes several plasma membrane amino
acid transporters by antagonizing their ubiquitin-mediated
degradation
Probable sulfate transport protein; sulfate uptake is mediated by
specific sulfate transporters Sul1p and Sul2p, which control the
concentration of endogenous activated sulfate intermediates
GTPase-activating protein for yeast Rab family members
including: Ypt7p (most effective), Ypt1p, Ypt31p, and Ypt32p
(in vitro); involved in vesicle mediated protein trafficking
Low affinity methionine permease, similar to Mup1p
Protein kinase with a possible role in MAP kinase signaling in
the pheromone response pathway
Protein that stimulates strand exchange by stabilizing the
binding of Rad51p to single-stranded DNA; involved in the
recombinational repair of double-strand breaks in DNA during
vegetative growth and meiosis; forms heterodimer with Rad57p
Saccharopine dehydrogenase (NADP+, L-glutamate-forming);
catalyzes the formation of saccharopine from alphaaminoadipate 6-semialdehyde, which is the seventh step in
lysine biosynthesis pathway
Protein involved in nitrosoguanidine resistance
NAD(+)-dependent glutamate dehydrogenase, degrades
glutamate to ammonia and alpha-ketoglutarate; expression
sensitive to nitrogen catabolite repression and intracellular
ammonia levels
ARF1(0,3) YDL193W SNF3(12,2) SEC31(6,4) YDL196W
ASF2(9,4) GGC1(0,4) YDL199C MGT1(3,0) TRM8(0,4)
MRPL11(0,4) YDL203C RTN2(0,5) HEM3(0,5) YDL206W
GLE1(4,5) NHP2(1,2) CWC2(1,2) UGA4(1,9) YDL211C
SHR3(1,3) NOP6(0,3)
Module genes
YDL210W
UGA4
YDL205C
HEM3
YPL201C
None
YDL227C
HO
GABA-specific transport protein
Phorphobilinogen deaminase, catalyzes the conversion of 4porphobilinogen to hydroxymethylbilane, the third step in the
heme biosynthetic pathway; localizes to both the cytoplasm and
nucleus; expression is regulated by Hap2p-Hap3p
Site-specific endonuclease required for gene conversion at the
MAT locus (homothallic switching) through the generation of a
ds DNA break; expression restricted to mother cells in late G1
as controlled by Swi4p-Swi6p, Swi5p and Ash1p
(64) MODULE 73
Genotype regulators
YGL063C-A PUS2(2,1) MRH4(0,1) ALG2(3,1) SGF73(6,1)
NPY1(1,1) MNP1(0,0) SRF3(1,0) RPB9(0,0) RCS1(8,1)
YGL072C HSF1(6,2) YGL074C MPS2(2,3)
YGL039W HEM2(0,1) YGL041C YGL041C-B YGL041W-A
YGL042C DST1(0,5) RNA15(1,3) RIM8(4,11) YGL046W
YGL047W RPT6(0,1) TIF4632(5,4) YGL050W MST27(8,49)
YGL052W PRM8(96,548) ERV14(0,233) OLE1(1,14)
SDS23(4,14) YGL057C RAD6(0,1) YGL059W
M7_375499_375499
M7_402833_415585
Module genes
YGL053W
PRM8
YOR027W
STI1
YGL051W
MST27
YGL057C
YNL007C
None
SIS1
YAR033W
MST28
YGL052W
(65) MODULE 75
None
YGL037C
PNC1
YGL099W
LSG1
YGL037C
PNC1
YER054C
GIP2
Pheromone-regulated protein with 2 predicted transmembrane
segments and an FF sequence, a motif involved in COPII
binding; forms a complex with Prp9p in the ER
Heat shock protein also induced by canavanine and entry into
stationary phase
Putative integral membrane protein, involved in vesicle
formation; forms complex with Mst28p; member of DUP240
gene family; binds COPI and COPII vesicles
HSP40 family chaperone; sit4 suppressor, dnaJ homolog
Putative integral membrane protein, involved in vesicle
formation; forms complex with Mst27p; member of DUP240
gene family; binds COPI and COPII vesicles
nicotinamidase
Putative GTPase involved in 60S ribosomal subunit biogenesis;
localized to the cytoplasm
nicotinamidase
YBR140C
IRA1
YCR040W
MATALPHA1
YHR122W
Module genes
YGL146C
YDR154C
YJR019C
None
None
None
TES1
YER041W
YEN1
YDR513W
YBR052C
YBR139W
TTR1
None
None
YGL038C
OCH1
YIR037W
HYR1
YDR077W
SED1
YDR535C
None
YDL023C
SRF4
YKR089C
STC1
YJL137C
GLG2
YKL162C
YGL081W
None
None
YBR203W
COS111
YMR110C
None
YPL221W
BOP1
YLL039C
UBI4
Pig1p, and Pig2p
Thioesterase; peroxisomal acyl-CoA thioesterase
Protein of unknown function, has similarity to endonuclease
Rth1p; potentially phosphorylated by Cdc28p
Glutaredoxin (thioltransferase) (glutathione reductase)
Mannosyltransferase of the cis-Golgi apparatus, initiates the
polymannose outer chain elongation of N-linked
oligosaccharides of glycoproteins
Thiol peroxidase that functions as a hydroperoxide receptor to
sense intracellular hydroperoxide levels and transduce a redox
signal to the Yap1p transcription factor
Isolated as a suppressor of an erd2 deletion mutant (ERD2 is the
HDEL receptor that sorts ER proteins), SED1 encodes a cell
wall protein.
ORF overlaps the verified gene GPD1; deletion in cyr1 mutant
results in loss of stress resistance
Protein of unknown function found in lipid particles; potential
Cdc28p substrate
Self-glucosylating initiator of glycogen synthesis, also
glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian
glycogenin
Protein required for wild-type resistance to the antifungal drug
ciclopirox olamine; not related to the COS family of
subtelomerically-encoded proteins
Protein of unknown function, overproduction suppresses a pam1
slv3 double null mutation
Ubiquitin, becomes conjugated to proteins, marking them for
selective degradation via the ubiquitin-26S proteasome system;
YDR343C
HXT6
YDL022W
YLR257W
GPD1
None
YJR059W
PTK2
YBR053C
YHR030C
None
SLT2
YAL060W
BDH1
YHR037W
PUT2
YIL065C
FIS1
YIL111W
COX5B
YOR176W
HEM15
YBR056W
None
YML004C
GLO1
YLL026W
HSP104
YJR085C
None
YFR053C
HXK1
YER067W
None
YCR030C
SYP1
YLR327C
YGR149W
YDR230W
YIL033C
None
None
None
BCY1
essential for the cellular stress response
High-affinity glucose transporter of the major facilitator
superfamily, nearly identical to Hxt7p, expressed at high basal
levels relative to other HXTs, repression of expression by high
glucose requires SNF3
glycerol-3-phosphate dehydrogenase
Putative serine/threonine protein kinase that enhances spermine
uptake; putative serine)/threonine kinase involved in spermine
metabolism
NAD-dependent (2R,3R)-2,3-butanediol dehydrogenase, a zinccontaining medium-chain alcohol dehydrogenase, produces 2,3butanediol from acetoin during fermentation and allows using
2,3-butanediol as a carbon source during aerobic growth
delta-1-pyrroline-5-carboxylate dehydrogenase
Mitochondrial outer membrane protein involved in membrane
fission, required for loalization of Dnm1p and Mdv1p during
mitochondrial division
Subunit Vb of cytochrome c oxidase, which is the terminal
chain; predominantly expressed during anaerobic growth while
its isoform Va (Cox5Ap) is expressed during aerobic growth
Ferrochelatase, a mitochondrial inner membrane protein,
catalyzes the insertion of ferrous iron into protoporphyrin IX,
the eighth and final step in the heme biosynthetic pathway;
Yfh1p mediates the use of iron by Hem15p
Monomeric glyoxalase I, catalyzes the detoxification of
methylglyoxal (a by-product of glycolysis) via condensation
with glutathione to produce S-D-lactoylglutathione; expression
regulated by methylglyoxal levels and osmotic stress
Heat shock protein that cooperates with Ydj1p (Hsp40) and
Ssa1p (Hsp70) to refold and reactivate previously denatured,
aggregated proteins; responsive to stresses including: heat,
ethanol, and sodium arsenite; involved in [PSI+] propagation
Hexokinase isoenzyme 1, cytosolic protein that catalyzes
phosphorylation of glucose during glucose metabolism,
expression is highest during growth on non-glucose carbon
sources and is repressed by Hxk2p
Protein with a potential role in actin cytoskeletal organization;
overexpression suppresses a pfy1 (profilin) null mutation
YOR136W
IDH2
YBR097W
VPS15
YCR075C
ERS1
YKL066W
None
YIL124W
AYR1
YOL063C
HUS1
YGR255C
COQ6
YBR149W
ARA1
YBR137W
None
YLR284C
ECI1
YHR092C
HXT4
YMR315W
YMR155W
None
None
YJL005W
CYR1
YGR223C
HSV2
YGL104C
VPS73
YBL064C
PRX1
YFR057W
None
YCR011C
ADP1
YOR386W
YKL036C
PHR1
None
Subunit of mitochondrial NAD(+)-dependent isocitrate
dehydrogenase, which catalyzes the oxidation of isocitrate to
alpha-ketoglutarate in the TCA cycle
Myristoylated Serine/threonine protein kinase involved in
vacuolar protein sorting
Protein with similarity to human cystinosin, which is a H(+)driven transporter involved in L-cystine export from lysosomes
and implicated in the disease cystinosis; contains seven
transmembrane domains
NADPH-dependent 1-acyl dihydroxyacetone phosphate
reductase found in lipid particles and ER; involved in
phosphatidic acid biosynthesis and required for spore
germination; capable of metabolizing mammalian steroid
hormones
Putative flavin-dependent monooxygenase, involved in
ubiquinone (Coenzyme Q) biosynthesis; located on the matrix
side of the mitochondrial inner membrane
Large subunit of NADP+ dependent arabinose dehydrogenase,
involved in carbohydrate metabolism; small subunit is
unidentified
Peroxisomal delta3,delta2-enoyl-CoA isomerase, hexameric
protein that converts 3-hexenoyl-CoA to trans-2-hexenoyl-CoA,
essential for the beta-oxidation of unsaturated fatty acids, oleateinduced
superfamily, expression is induced by low levels of glucose and
repressed by high levels of glucose
Phosphatidylinositol 3,5-bisphosphate-binding protein, predicted
to fold as a seven-bladed beta-propeller; displays punctate
cytoplasmic localization
None
Mitochondrial peroxiredoxin (1-Cys Prx) with thioredoxin
peroxidase activity, has a role in reduction of hydroperoxides;
induced during respiratory growth and under conditions of
oxidative stress
Shows homology to ATP-dependent permeases; Active transport
ATPase
photolyase
YPL203W
TPK2
YKL067W
YNK1
YJR020W
None
YOR374W
ALD4
YJL214W
HXT8
YNR001C
YHR097C
CIT1
None
YDR272W
GLO2
YDL106C
PHO2
YER177W
BMH1
YGR244C
LSC2
YJL068C
YJL164C
None
TPK1
YPL003W
ULA1
YKL035W
UGP1
YCR091W
KIN82
YML110C
COQ5
YDL110C
YOR135C
None
None
YBL015W
ACH1
YMR152W
YIM1
YMR136W
GAT2
YCL040W
GLK1
Involved in nutrient control of cell growth and division; cAMPdependent protein kinase catalytic subunit
Nucleoside diphosphate kinase, catalyzes the phosphorylation of
nucleoside diphosphates into the corresponding triphosphates for
nucleic acid biosynthesis
Mitochondrial aldehyde dehydrogenase that utilizes NADP+ or
NAD+ equally as coenzymes; expression is glucose repressed
citrate synthase. Nuclear encoded mitochondrial protein.
Cytoplasmic glyoxalase II, catalyzes the hydrolysis of S-Dlactoylglutathione into glutathione and D-lactate
Homeobox transcription factor; regulatory targets include genes
involved in phosphate metabolism; binds cooperatively with
Pho4p to the PHO5 promoter; phosphorylation of Pho2p
facilitates interaction with Pho4p
others
Beta subunit of succinyl-CoA ligase, which is a mitochondrial
enzyme of the TCA cycle that catalyzes the nucleotidedependent conversion of succinyl-CoA to succinate
Protein that acts together with Uba3p to activate Rub1p before
its conjugation to proteins (neddlyation), which may play a role
in protein degradation
UDP-glucose pyrophosphorylase or UTP-glucose-1-phosphate
uridylyltransferase, EC:2.7.7.9
kinase C subfamily
2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase,
involved in ubiquinone (Coenzyme Q) biosynthesis; located in
mitochondria
Acetyl-coA hydrolase, primarily localized to mitochondria;
required for acetate utilization and for diploid pseudohyphal
growth
Mitochondrial inner membrane protease, similar to E. coli leader
peptidase
Protein containing GATA family zinc finger motifs; similar to
Gln3p and Dal80p; expression repressed by leucine
Glucokinase, catalyzes the phosphorylation of glucose at C6 in
YCR004C
YCP4
YDR342C
HXT7
YFR015C
GSY1
YOR142W
LSC1
the first irreversible step of glucose metabolism; one of three
glucose phosphorylating enzymes; expression regulated by nonfermentable carbon sources
Protein of unknown function, has sequence and structural
similarity to flavodoxins; green fluorescent protein (GFP)-fusion
protein localizes to the cytoplasm in a punctate pattern
superfamily, nearly identical to Hxt6p, expressed at high basal
levels relative to other HXTs, expression repressed by high
glucose levels
Glycogen synthase with similarity to Gsy2p, the more highly
expressed yeast homolog; expression induced by glucose
limitation, nitrogen starvation, enviromental stress, and entry
into stationary phase
Alpha subunit of succinyl-CoA ligase, which is a mitochondrial
enzyme of the TCA cycle that catalyzes the nucleotidedependent conversion of succinyl-CoA to succinate
(66) MODULE 76
YKL101W
HSL1
YKR099W
BAS1
YML027W
YOX1
YIL119C
RPI1
YMR001C
CDC5
YPL256C
Genotype regulators
CLN2
Nim1p-related protein kinase that regulates the morphogenesis
and septin checkpoints; associates with the assembled septin
filament; required along with Hsl7p for bud neck recruitment,
phosphorylation, and degradation of Swe1p
Homeodomain-containing transcriptional repressor, binds to
Mcm1p and to early cell cycle boxes (ECBs) in the promoters of
cell cycle-regulated genes expressed in M/G1 phase; expression
is cell cycle-regulated; potential Cdc28p substrate
DCS1(0,4) YLR271W
M12_659357_674651
Module genes
YDR024W
FYV1
YLR205C
HMX1
conserved in closely related Saccharomyces species; mutation
decreases survival upon exposure to K1 killer toxin
ER localized, heme-binding peroxidase involved in the
degradation of heme; does not exhibit heme oxygenase activity
despite similarity to heme oxygenases; expression regulated by
AFT1
YLR056W
ERG3
YLR101C
None
YMR061W
RNA14
YMR009W
None
YLR100W
ERG27
YGR060W
ERG25
YML008C
ERG6
YNL017C
None
YER044C
ERG28
YMR015C
ERG5
YHR039C
MSC7
YMR134W
None
YHR190W
ERG9
YGR049W
SCM4
YMR202W
ERG2
YNR019W
ARE2
YNR043W
MVD1
YHR007C
ERG11
C-5 sterol desaturase, catalyzes the introduction of a C-5(6)
double bond into episterol, a precursor in ergosterol
biosynthesis; mutants are viable, but cannot grow on nonfermentable carbon sources
Cleavage and polyadenylation factor I (CF I) component
involved in cleavage and polyadenylation of mRNA 3' ends;
bridges interaction between Rna15p and Hrp1p in the CF I
complex
3-keto sterol reductase, catalyzes the last of three steps required
to remove two C-4 methyl groups from an intermediate in
ergosterol biosynthesis; mutants are sterol auxotrophs
C-4 methyl sterol oxidase, catalyzes the first of three steps
required to remove two C-4 methyl groups from an intermediate
in ergosterol biosynthesis; mutants accumulate the sterol
intermediate 4,4-dimethylzymosterol
Delta(24)-sterol C-methyltransferase, converts zymosterol to
fecosterol in the ergosterol biosynthetic pathway by methylating
position C-24
Endoplasmic reticulum membrane protein, may facilitate
protein-protein interactions between the Erg26p dehydrogenase
and the Erg27p 3-ketoreductase and/or tether these enzymes to
the ER
C-22 sterol desaturase, a cytochrome P450 enzyme that
catalyzes the formation of the C-22(23) double bond in the sterol
side chain in ergosterol biosynthesis; may be a target of azole
antifungal drugs
Protein of unknown function, green fluorescent protein (GFP)fusion protein localizes to the endoplasmic reticulum; msc7
mutants are defective in directing meiotic recombination events
to homologous chromatids
Farnesyl-diphosphate farnesyl transferase (squalene synthase),
joins two farnesyl pyrophosphate moieties to form squalene in
the sterol biosynthesis pathway
Protein that suppresses ts allele of CDC4 when overexpressed
C-8 sterol isomerase, catalyzes the isomerization of the delta-8
double bond to the delta-7 position at an intermediate step in
ergosterol biosynthesis
Acyl-CoA:sterol acyltransferase, isozyme of Are1p;
endoplasmic reticulum enzyme that contributes the major sterol
esterification activity in the presence of oxygen
involved in the polyisoprene biosynthesis pathway; mevalonate
pyrophosphate decarboxylase
Lanosterol 14-alpha-demethylase, catalyzes the C-14
demethylation of lanosterol to form 4,4''-dimethyl cholesta8,14,24-triene-3-beta-ol in the ergosterol biosynthesis pathway;
member of the cytochrome P450 family
YIR024C
None
YER145C
FTR1
YJR048W
CYC1
YGR235C
YGR266W
None
None
YGL055W
OLE1
YEL033W
None
YGR234W
YHB1
YML126C
ERG13
YPL117C
IDI1
YNL111C
CYB5
YJL167W
ERG20
YMR208W
ERG12
YML075C
HMG1
YEL034W
HYP2
YPL028W
ERG10
YLL012W
YEH1
YJR047C
ANB1
YDL086W
None
YLR153C
ACS2
YGL001C
ERG26
High affinity iron permease involved in the transport of iron
across the plasma membrane; forms complex with Fet3p;
expression is regulated by iron
Cytochrome c, isoform 1; electron carrier of the mitochondrial
intermembrane space that transfers electrons from ubiquinonecytochrome c oxidoreductase to cytochrome c oxidase during
cellular respiration
Fatty acid desaturase, required for monounsaturated fatty acid
synthesis and for normal distribution of mitochondria
may play a role in the oxidative stress response;
Flavohemoglobin
3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase,
catalyzes the formation of HMG-CoA from acetyl-CoA and
acetoacetyl-CoA; involved in the second step in mevalonate
biosynthesis
Isopentenyl diphosphate:dimethylallyl diphosphate isomerase
(IPP isomerase), catalyzes an essential activation step in the
isoprenoid biosynthetic pathway; required for viability
cytochrome b5
Farnesyl pyrophosphate synthetase, has both
dimethylallyltranstransferase and geranyltranstransferase
activities; catalyzes the formation of C15 farnesyl
pyrophosphate units for isoprenoid and sterol biosynthesis
Mevalonate kinase, acts in the biosynthesis of isoprenoids and
sterols, including ergosterol, from mevalonate
One of two isozymes of HMG-CoA reductase that catalyzes the
conversion of HMG-CoA to mevalonate, which is a rate-limiting
step in sterol biosynthesis; localizes to the nuclear envelope;
overproduction induces the formation of karmellae
Translation initiation factor eIF-5A, promotes formation of the
first peptide bond; similar to and functionally redundant with
Anb1p; undergoes an essential hypusination modification;
expressed under aerobic conditions
Acetyl-CoA C-acetyltransferase (acetoacetyl-CoA thiolase),
cytosolic enzyme that transfers an acetyl group from one acetylCoA molecule to another, forming acetoacetyl-CoA; involved in
the first step in mevalonate biosynthesis
Hypothetical ORF
Translation initiation factor eIF-5A, promotes formation of the
first peptide bond; similar to and functionally redundant with
Hyp2p; undergoes an essential hypusination modification;
expressed under anaerobic conditions
one of 2 acetyl-coA synthetases in yeast; acetyl-coenzyme A
synthetase
C-3 sterol dehydrogenase, catalyzes the second of three steps
YHR072W
ERG7
required to remove two C-4 methyl groups from an intermediate
in ergosterol biosynthesis
Lanosterol synthase, an essential enzyme that catalyzes the
cyclization of squalene 2,3-epoxide, a step in ergosterol
biosynthesis
(67) MODULE 77
Genotype regulators
SUI2(0,2) YJR008W TDH2(0,8) SPC1(0,1) MET3(0,24)
YJR011C YJR012C GPI14(2,4) RBF22 YJR015W ILV3(1,3)
ESS1(1,0) YJR018W TES1(0,1) YJR020W REC107(108,2)
LSM8(0,2) YJR023C YJR024C BNA1(1,78) YJR026W
M10_461201_464261
Module genes
YNR011C
PRP2
YJR015W
(68) MODULE 78
YMR036C
Genotype regulators
None
MIH1
EDC3(0,0) YEL016C PMP2(0,0) GTT3(1,0) YEL018C-A
EAF5(0,0) MMS21(1,0) YEL020C YEL020C-B TIM9(0,3)
URA3(222,250) GEA2(5,1) YEL023C RIP1(1,5) YEL025C
SNU13(0,1) CUP5(0,0)
M5_109310_117705
Module genes
YLR420W
URA4
YMR241W
YHM2
YER088C
DOT6
YOL126C
MDH2
YJL130C
URA2
YOL143C
RIB4
YNL018C
None
YNL065W
AQR1
YKL216W
URA1
(69) MODULE 79
RNA-dependent ATPase in the DEAH-box family, required for
activation of the spliceosome before the first transesterification
step in RNA splicing
Third step in pyrimidine biosynthesis pathway; dihydrooratase
Yeast suppressor gene of HM mutant (abf2); DNA-binding
protein, mtDNA stabilizing protein, mitochondrial inner
membrane protein with low homology to RIM2
Protein of unknown function, involved in telomeric gene
silencing and filamentation
Cytoplasmic malate dehydrogenase, catalyzes interconversion of
malate and oxaloacetate; involved in gluconeogenesis and
glyoxylate cycle
Multifunctional carbamoylphosphate synthetase (CPSase)aspartate transcarbamylase (ATCase) that catalyzes the two first
reactions of the pyrimidine pathway; carbamoyl-phophate
synthetase, aspartate transcarbamylase, and glutamine
amidotransferase
Lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase,
also known as DMRL synthase); catalyzes synthesis of
immediate precursor to riboflavin
Plasma membrane transporter of the major facilitator
superfamily that confers resistance to short-chain
monocarboxylic acids and quinidine
The enzyme catalyzes the conversion of dihydroorotic acid to
orotic acid; dihydroorotate dehydrogenase
YJL056C
ZAP1
YPL075W
GCR1
YGL014W
Genotype regulators
PUF4
YJL043W GYP6(4,4) YJL045W YJL046W RTT101(1,0)
YJL047C-A UBX6(0,8) YJL049W MTR4(5,11) YJL051W
YJL052C-A TDH1(1,1) PEP8(2,1) TIM54(1,3) YJL055W
ZAP1(10,2) YJL057C BIT61(4,2)
M10_336317_353027
Module genes
YAR023C
YGL258W
zinc-finger domains
None
None
YDR284C
DPP1
YNL254C
YOR387C
None
None
YOL154W
ZPS1
YKL175W
ZRT3
YIL045W
PIG2
YGL256W
ADH4
YPL104W
MSD1
Diacylglycerol pyrophosphate (DGPP) phosphatase, zincregulated vacuolar membrane-associated lipid phosphatase,
dephosphorylates DGPP to phosphatidate (PA) and Pi, then PA
to diacylglycerol; involved in lipid signaling and cell
metabolism
Putative GPI-anchored protein; transcription is induced under
low-zinc conditions, as mediated by the Zap1p transcription
factor, and at alkaline pH
Vacuolar membrane zinc transporter, transports zinc from
storage in the vacuole to the cytoplasm when needed;
transcription is induced under conditions of zinc deficiency
Interacts with Gsy2p; Protein with 30% identity to protein
corresponding to YER054
Alcohol dehydrogenase type IV, dimeric enzyme demonstrated
to be zinc-dependent despite sequence similarity to ironactivated alcohol dehydrogenases; transcription is induced in
response to zinc deficiency; alcohol dehydrogenase isoenzyme
IV
Mitochondrial aspartyl-tRNA synthetase, required for acylation
of aspartyl-tRNA; yeast and bacterial aspartyl-, asparaginyl-,
and lysyl-tRNA synthetases contain regions with high sequence
similarity, suggesting a common ancestral gene
(70) MODULE 80
Genotype regulators
SPO75(2,1) MMM1(104,0) YLL006W-A YLL007C DRS1(1,0)
COX17(0,0) PSR1(5,8) SOF1(0,6) YEH1(4,5) PUF3(226,5)
YLL014W
M12_131338_131338
Module genes
YLL007C
None
YLL013C
PUF3
member of the PUF protein family, which is named for the
founding members, PUmilio and Fbf
(71) MODULE 81
YDR213W
UPC2
YDL230W
PTP1
YGL229C
SAP4
Module genes
YOR393W
YNR073C
YCR007C
YBL095W
ERR1
None
None
None
YJR150C
DAN1
YOR010C
TIR2
YMR153C-A
(72) MODULE 83
None
YDR264C
AKR1
YJR122W
CAF17
YER028C
MIG3
YIR017C
MET28
YBR150C
TBS1
YCL055W
KAR4
YHR099W
TRA1
Module genes
YOR187W
YNL185C
YDR114C
YBR268W
TUF1
MRPL19
None
MRPL37
YOR020C
HSP10
involved in sterol uptake; zinc finger transcription factor of the
Zn(2)-Cys(6) binuclear cluster domain type
Protein required for function of the Sit4p protein phosphatase,
member of a family of similar proteins that form complexes with
Sit4p, including Sap155p, Sap185p, and Sap190p
Protein of unknown function, has similarity to enolases
Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p,
and Tir4p; expressed under anaerobic conditions, completely
repressed during aerobic growth
Cold shock-induced protein of the Srp1p/Tip1p family of serinealanine-rich proteins
proteins
Probable transcriptional repressor involved in response to toxic
agents such as hydroxyurea that inhibit ribonucleotide reductase;
phosphorylation by Snf1p or the Mec1p pathway inactivates
Mig3p, allowing induction of damage response genes
Histone acetyltransferase component, putative ortholog of
human TRRAP which is an essential cofactor of c-Myc
Translation elongation factor Tu, mitochondrial
Mitochondrial ribosomal protein of the large subunit
Mitochondrial matrix co-chaperonin that inhibits the ATPase
activity of Hsp60p, a mitochondrial chaperonin; involved in
YPR166C
MRP2
YCR046C
IMG1
YJL104W
PAM16
YLR259C
HSP60
YGR181W
TIM13
YIL098C
FMC1
YPR099C
None
YLR139C
SLS1
YDR296W
MHR1
YJL131C
None
YGR082W
TOM20
YER174C
GRX4
YOR286W
FMP31
YLL009C
COX17
YEL020W-A
TIM9
YPR133W-A
TOM5
YOR334W
MRS2
YPL183W-A
YHR005C-A
None
MRS11
protein folding and sorting in the mitochondria; 10 kD heat
shock protein with similarity to E. coli groES
Mitochondrial ribosomal protein of the small subunit
Mitochondrial ribosomal protein of the small subunit, required
for respiration and for maintenance of the mitochondrial genome
Constituent of the mitochondrial import motor associated with
the presequence translocase, along with Ssc1p, Tim44p, Mge1p,
and Pam18p; has similarity to J-domain containing proteins
Tetradecameric mitochondrial chaperonin required for ATPdependent folding of precursor polypeptides and complex
assembly; prevents aggregation and mediates protein refolding
after heat shock; role in mtDNA transmission; similarity to
groEL
Translocase of the inner membrane; mitochondrial
intermembrane space protein mediating import and insertion of
polytopic inner membrane proteins; Subunit of mitochondrial
protein import machinery
Mitochondrial matrix protein, required for assembly or stability
at high temperature of the F1 sector of mitochondrial F1F0 ATP
synthase
Mitochondrial membrane protein required for assembly of
respiratory-chain enzyme complexes III and IV; coordinates
expression of mitochondrially-encoded genes; may facilitate
delivery of mRNA to membrane-bound translation machinery
Protein involved in mitochondrial homologous DNA
recombination and in transcription regulation; binds to
activation domains of acidic activators; presence in RNA pol II
holoenzyme may help recruit an Ssn3p-active form of the
Translocase of Outer Mitochondrial membrane; 20 kDa
mitochondrial outer membrane protein import receptor
Hydroperoxide and superoxide-radical responsive glutathionedependent oxidoreductase; monothiol glutaredoxin subfamily
member along with Grx3p and Grx5p; protects cells from
oxidative damage
mitochondria
Copper metallochaperone that shuttles copper from the cytosol
to the mitochondrial intermembrane space for delivery to
cytochrome c oxidase
Mitochondrial intermembrane space protein mediating import
and insertion of polytopic inner membrane proteins
Translocase of the Outer Mitochondrial membrane; Membrane
protein involved in protein translocation to the mitochondria
Mitochondrial inner membrane Mg(2+) channel, required for
maintenance of intramitochondrial Mg(2+) concentrations at the
correct level to support splicing of group II introns
Essential protein of the mitochondrial intermembrane space,
forms a complex with Tim9p (TIM10 complex) that mediates
insertion of hydrophobic proteins at the inner membrane, has
homology to Mrs5p, which is also involved in this process
(73) MODULE 84
YFR009W
GCN20
YOR337W
TEA1
YJR122W
CAF17
YDR283C
GCN2
YDR225W
HTA1
YKL109W
HAP4
YKL109W
HAP4
Module genes
YPL097W
YMR193W
YDR337W
MSY1
MRPL24
MRPS28
YNL083W
SAL1
YCR003W
YBR251W
YLR382C
MRPL32
MRPS5
NAM2
YHR116W
COX23
YPL173W
YDR237W
MRPL40
MRPL7
YDR375C
BCS1
uncharged tRNA
proteins
Tyrosyl-tRNA synthetase
Probable transporter, member of the Ca2+-binding subfamily of
the mitochondrial carrier family, with two EF-hand motifs;
Pet9p and Sal1p have an overlapping function critical for
viability; polymorphic in different S. cerevisiae strains
mitochondrial leucyl tRNA synthetase
Protein that functions in mitochondrial copper homeostasis and
is essential for functional cytochrome oxidase expression;
homologous to COX17, localized to the mitochondrial
intermembrane space
Protein of the mitochondrial inner membrane that functions as
an ATP-dependent chaperone, required for the assembly of the
cytochrome bc(1) complex from the Rip1p and Qcr10p proteins;
YDR494W
RSM28
YER182W
FMP10
YBR120C
YNL177C
CBP6
MRPL22
YBR185C
MBA1
YJL096W
YKL138C
YER058W
YDL202W
YKR085C
YLR204W
MRPL49
MRPL31
PET117
MRPL11
MRPL20
QRI5
YPL029W
SUV3
YIR021W
MRS1
YDR175C
YMR286W
YDR462W
RSM24
MRPL33
MRPL28
YNL137C
NAM9
YNL081C
SWS2
YLR312W-A
MRPL15
YBR192W
RIM2
YDR041W
RSM10
YIL093C
YBR037C
YGR028W
YLR253W
RSM25
SCO1
MSP1
None
YKL087C
CYT2
YKL167C
MRP49
YHR109W
CTM1
YGL143C
MRF1
member of the CDC48/PAS1/SEC18 ATPase family
mitochondria
Translational activator of COB mRNA
Protein involved in assembly of mitochondrial respiratory
complexes; may act as a receptor for proteins destined for export
from the mitochondrial matrix to the inner membrane
Protein required for assembly of cytochrome c oxidase
Mitochondrial protein of unknown function
ATP-dependent RNA helicase, component of the mitochondrial
degradosome along with the RNase Msu1p; the degradosome
associates with the ribosome and mediates turnover of aberrant
or unprocessed RNAs
Protein required for the splicing of two mitochondrial group I
introns (BI3 in COB and AI5beta in COX1); forms a splicing
complex, containing four subunits of Mrs1p and two subunits of
the BI3-encoded maturase, that binds to the BI3 RNA
Mitochondrial ribosomal protein of the small subunit; can
mutate to suppress nonsense mutations in mitochondrial genes
Putative mitochondrial ribosomal protein of the small subunit,
has similarity to E. coli S13 ribosomal protein
Protein of the mitochondrial carrier (MCF) family that is
required for respiration; Probable carrier protein, mitochondrial
Mitochondrial ribosomal protein of the small subunit, has
similarity to E. coli S10 ribosomal protein; essential for
viability, unlike most other mitoribosomal proteins
inner mitochondrial membrane protein
40 kDa putative membrane-spanning ATPase
links heme covalently to apocytochrome c1; cytochrome c1
heme lyase
Mitochondrial ribosomal protein of the large subunit, not
essential for mitochondrial translation
Cytochrome c lysine methyltransferase, trimethylates residue 72
of apo-cytochrome c (Cyc1p) in the cytosol; not required for
normal respiratory growth
Mitochondrial polypeptide chain release factor, involved in stop
YMR158W
YFR007W
YER087W
MRPS8
None
None
YJL112W
MDV1
YHR147C
MRPL6
YHR091C
MSR1
YGL107C
YMR188C
YDR322W
YNL005C
YDL107W
YPR100W
RMD9
MRPS17
MRPL35
MRP7
MSS2
MRPL51
YGR062C
COX18
YBR262C
FMP51
YLR239C
LIP2
YGR165W
MRPS35
YPL118W
MRP51
YML129C
COX14
YOR354C
MSC6
YOL033W
MSE1
YPL172C
COX10
YNR020C
None
YKL170W
MRPL38
YGL236C
MTO1
codon recognition and hydrolysis of the peptidyl-tRNA bond
during mitochondrial translation; lack of MRF1 causes
mitochondrial genome instability
WD repeat protein that regulates steps in the Dnm1p-dependent
process of mitochondrial fission
Nuclear-encoded mitochondrial protein; Arginyl-tRNA
synthetase
Mitochondrial protein required for sporulation
cox1 pre-mRNA splicing factor
Mitochondrial inner membrane protein, required for export of
the Cox2p C terminus from the mitochondrial matrix to the
intermembrane space during its assembly into cytochrome c
oxidase; similar to Oxa2p of N.crassa
mitochondria
Lipoyl ligase, involved in the modification of mitochondrial
enzymes by the attachment of lipoic acid groups
Mitochondrial ribosomal protein of the large subunit; MRP51
exhibits genetic interactions with mutations in the COX2 and
COX3 mRNA 5'-untranslated leader sequences
Mitochondrial membrane protein, required for assembly of
cytochrome c oxidase
Protein of unknown function, green fluorescent protein (GFP)fusion protein localizes to mitochondria; msc6 mutants are
defective in directing meiotic recombination events to
homologous chromatids
Mitochondrial glutamyl-tRNA synthetase, encoded by a nuclear
gene
Heme A:farnesyltransferase, catalyzes the first step in the
conversion of protoheme to the heme A prosthetic group
required for cytochrome c oxidase activity; human ortholog is
associated with mitochondrial disorders
Mitochondrial ribosomal protein of the large subunit; appears as
two protein spots (YmL34 and YmL38) on two-dimensional
SDS gels
Mitochondrial protein required for respiration in paromomycinresistant 15S rRNA mutants; forms a heterodimer complex with
Mss1p that plays a role in optimizing mitochondrial protein
synthesis
YBL090W
MRP21
YMR267W
PPA2
YDR347W
MRP1
YPR125W
None
YKL053C-A
MDM35
YHR038W
RRF1
YBL038W
YML009C
MRPL16
MRPL39
YJR113C
RSM7
YDR511W
ACN9
YNL122C
None
YEL050C
RML2
YBR122C
MRPL36
YNL073W
MSK1
YDR116C
MRPL1
YKL195W
MIA40
YGL235W
None
YKR006C
MRPL13
YIL070C
MAM33
YJL063C
YGR021W
MRPL8
None
YMR257C
PET111
YPL215W
CBP3
Mitochondrial ribosomal protein of the large subunit; MRP21
exhibits genetic interactions with mutations in the COX2 and
COX3 mRNA 5'-untranslated leader sequences
Mitochondrial inorganic pyrophosphatase, required for
mitochondrial function and possibly involved in energy
generation from inorganic pyrophosphate
Mitochondrial ribosomal protein of the small subunit; MRP1
exhibits genetic interactions with PET122, encoding a COX3specific translational activator, and with PET123, encoding a
small subunit mitochondrial ribosomal protein
Mitochondrial Distribution and Morphology; Similar to human
sequence predicted by GENSCAN
Ribosomal Recycling Factor 1; originally characterized as FIL1,
a Factor for Isocitrate Lyase expression; mitochondrial ribosome
recycling factor
similarity to E. coli S7 ribosomal protein
Protein of the mitochondrial intermembrane space, required for
acetate utilization and gluconeogenesis; has orthologs in higher
eukaryotes
Mitochondrial ribosomal protein of the large subunit, has
similarity to E. coli L2 ribosomal protein; fat21 mutant allele
causes inability to utilize oleate and may interfere with activity
of the Adr1p transcription factor
Mitochondrial ribosomal protein of the large subunit;
overproduction suppresses mutations in the COX2 leader
peptide-encoding region
Mitochondrial lysine-tRNA synthetase, required for import of
both aminoacylated and deacylated forms of tRNA(Lys) into
mitochondria
Essential protein of the mitochondrial intermembrane space,
involved in import and assembly of intermembrane space
proteins
Mitochondrial ribosomal protein of the large subunit, not
essential for mitochondrial translation
Acidic protein of the mitochondrial matrix involved in oxidative
phosphorylation; related to the human complement receptor
gC1q-R
Specific translational activator for the COX2 mRNA, located in
the mitochondrial inner membrane
Protein required for assembly of ubiquinol cytochrome-c
reductase complex (cytochrome bc1 complex); involved in
YLR439W
MRPL4
YNL315C
ATP11
YBR282W
MRPL27
YMR157C
FMP39
YHR059W
FYV4
YGL069C
SRF3
YER078C
YJL046W
YKL169C
None
None
None
YGL129C
RSM23
YNR040W
None
YOR266W
PNT1
YNL284C
MRPL10
YNL306W
MRPS18
YJL180C
ATP12
YGR076C
YGR084C
YBR146W
YDR316W
MRPL25
MRP13
MRPS9
OMS1
YGL068W
MNP1
YHL004W
YML087C
MRP4
None
YOR158W
PET123
YLR008C
PAM18
YNL184C
None
cytochrome-c reductase assembly
Molecular chaperone, required for the assembly of alpha and
beta subunits into the F1 sector of mitochondrial F1F0 ATP
synthase
mitochondria
exposure to K1 killer toxin
ORF overlaps the uncharacterized ORF YGL068W; deletion in
cyr1 mutant results in loss of stress resistance
similarity to mammalian apoptosis mediator proteins; null
mutation prevents induction of apoptosis by overproduction of
metacaspase Mca1p
Involved in targeting of proteins to the mitochondrial inner
membrane; Pentamidine resistance protein; involved in
pentamidine resistance protein
Mitochondrial ribosomal protein of the large subunit; appears as
two protein spots (YmL10 and YmL18) on two-dimensional
SDS gels
Mitochondrial ribosomal protein of the small subunit; essential
for viability, unlike most other mitoribosomal proteins
Molecular chaperone, required for the assembly of alpha and
beta subunits into the F1 sector of mitochondrial F1F0 ATP
synthase
None
Putative mitochondrial-nucleoid specific ribosomal protein;
Mitochondrial ribosomal protein of the small subunit; PET123
exhibits genetic interactions with PET122, which encodes a
COX3 mRNA-specific translational activator
Constituent of the mitochondrial import motor associated with
the presequence translocase, along with Ssc1p, Tim44p, Mge1p,
and Pam16p; stimulates the ATPase activity of Ssc1p to drive
mitochondrial import; contains a J domain
YCR024C
None
YOL071W
EMI5
YMR098C
None
YER050C
RSM18
YDR194C
MSS116
YNL252C
YGR220C
YLR069C
MRPL17
MRPL9
MEF1
YHR011W
DIA4
YMR166C
None
YHR198C
FMP22
YDR430C
CYM1
YJR101W
YOR150W
YOL023W
YGR169C
YMR024W
YKL194C
(74) MODULE 85
RSM26
MRPL23
IFM1
PUS6
MRPL3
MST1
YBR158W
AMN1
YJL098W
SAP185
Non-essential protein of unknown function required for
transcriptional induction of the early meiotic-specific
transcription factor IME1, also required for sporulation
similarity to E. coli S18 ribosomal protein
Mitochondrial RNA helicase of the DEAD box family,
necessary for splicing of several mitochondrial introns
mitochondrial elongation factor G-like protein
Probable mitochondrial seryl-tRNA synthetase, mutant displays
increased invasive and pseudohyphal growth
mitochondria
Cytosolic metalloprotease; computational analysis of large-scale
protein-protein interaction data suggests a possible role in
pyruvate metabolism
Mitochondrial translation initiation factor 2
RNA:Psi-synthase
mitochondrial threonine-tRNA synthetase
Genotype regulators
ECM32(5,17) BMH1(0,3) PDA1(0,1) DMC1(44,9) ISC10(6,4)
SLO1(0,9) YER181C FMP10(2,4) FAU1(1,31) YER184C
YER185W YER186C YER186W-A YER187W YER188C-A
YER188W YER189W YER190C-A YER190C-B YRF12(809,5)
M5_553222_568734
Module genes
YLL065W
YDR543C
YKL225W
YNL337W
YNR077C
YER188W
YJR162C
None
None
None
None
None
None
None
YFL063W
(75) MODULE 86
None
YJL089W
SIP4
YGL037C
PNC1
YPL204W
HRR25
YJL089W
SIP4
YDR259C
Genotype regulators
YAP6
transcription
nicotinamidase
Similar to YCK1 and YCK2, two other casein kinase I isoforms;
found primarily in nucleus; may be involved in DNA-damage
repair; casein kinase I isoform
transcription
YCL012C YCL012W YCL013W BUD3(10,152) DCC1(2,9)
NFS1(40,7) LEU2(246,526) YCL019W YCL020W YCL021W
YCL021W-A YCL022C YCL023C KCC4(6,2) AGP1(6,1)
YCL026C FRM2(1,3) YCL026C-B FUS1(0,1) RNQ1(0,0)
BIK1(0,0) YCLX06C YCLX07W YCLX08C YCLX09W
YCLX10C
M3_79091_92391
Module genes
YGL138C
None
YPL181W
CTI6
YKL120W
OAC1
YCR005C
CIT2
YJR016C
ILV3
YGR146C
YGL062W
None
PYC1
YFL021W
GAT1
YOR226C
ISU2
YLR348C
DIC1
Protein that relieves transcriptional repression by binding to the
Cyc8p-Tup1p corepressor and recruiting the SAGA complex to
the repressed promoter; contains a PHD finger domain
Mitochondrial inner membrane transporter, transports
oxaloacetate, sulfate, and thiosulfate; member of the
mitochondrial carrier family
non-mitochondrial citrate synthase
Dihydroxyacid dehydratase, catalyzes third step in the common
pathway leading to biosynthesis of branched-chain amino acids
converts pyruvate to oxaloacetate; pyruvate carboxylase
Transcriptional activator of genes involved in nitrogen catabolite
repression, member of the GATA family of DNA binding
proteins; activity and localization regulated by nitrogen
limitation and Ure2p
Conserved protein of the mitochondrial matrix, required for
synthesis of mitochondrial and cytosolic iron-sulfur proteins,
performs a scaffolding function in mitochondria during Fe/S
cluster assembly; isu1 isu2 double mutant is inviable
Mitochondrial dicarboxylate carrier, integral membrane protein,
catalyzes a dicarboxylate-phosphate exchange across the inner
mitochondrial membrane, transports cytoplasmic dicarboxylates
into the mitochondrial matrix
YGL010W
None
YOR375C
GDH1
YKL030W
YOR225W
YOR271C
None
None
None
YKR071C
DRE2
YAL062W
GDH3
YCL017C
NFS1
YGL009C
LEU1
YER073W
ALD5
YBR068C
BAP2
YLR149C
None
YKL029C
MAE1
YMR108W
ILV2
YPL269W
KAR9
YHR208W
BAT1
NADP(+)-dependent glutamate dehydrogenase, synthesizes
glutamate from ammonia and alpha-ketoglutarate; rate of alphaketoglutarate utilization differs from Gdh3p; expression
regulated by nitrogen and carbon sources
Protein of unknown function; mutation displays synthetic lethal
interaction with the pol3-13 allele of CDC2
NADP(+)-dependent glutamate dehydrogenase, synthesizes
glutamate from ammonia and alpha-ketoglutarate; rate of alphaketoglutarate utilization differs from Gdh1p; expression
regulated by nitrogen and carbon sources
Required for the post-transcriptional thio-modification of both
mitochondrial and cytoplasmic tRNAs, also functions in
mitochondrial iron-sulfur cluster biogenesis; NifS-like protein
Isopropylmalate isomerase, catalyzes the second step in the
leucine biosynthesis pathway
Mitochondrial aldehyde dehydrogenase that is activated by K+
and utilizes NADP+ as the preferred coenzyme
High-affinity leucine permease, functions as a branched-chain
amino acid permease involved in the uptake of leucine,
isoleucine and valine; contains 12 predicted transmembrane
domains
Mitochondrial malic enzyme, catalyzes the oxidative
decarboxylation of malate to pyruvate, which is a key
intermediate in sugar metabolism and a precursor for synthesis
of several amino acids
Acetolactate synthase, localizes in the mitochondria; expression
of the gene is under general amino acid control
Karyogamy protein required for correct positioning of the
mitotic spindle and for orienting cytoplasmic microtubules,
localizes at the shmoo tip in mating cells and at the tip of the
growing bud in small-budded cells through anaphase
Mitochondrial branched-chain amino acid aminotransferase,
homolog of murine ECA39; highly expressed during logarithmic
phase and repressed during stationary phase
(76) MODULE 87
YMR179W
SPT21
YMR019W
STB4
YKL032C
IXR1
COX5b
YHL028W
WSC4
YDR224C
HTB1
YCL055W
KAR4
YBL052C
Module genes
YDR112W
YIL130W
SAS3
cell wall integrity and stress response component 4; Putative
integral membrane protein containing novel cysteine motif.
Similarity to SLG1 (WSC1), WSC2 and WSC3
methylation
None
None
YDL070W
BDF2
YBR049C
REB1
YOL149W
DCP1
YLR183C
TOS4
YKL101W
HSL1
YDR111C
YPL256C
ALT2
CLN2
YJL187C
SWE1
YML053C
None
YDL003W
MCD1
YPL255W
BBP1
Protein involved in transcription initiation at TATA-containing
promoters; associates with the basal transcription factor TFIID;
contains two bromodomains; corresponds to the C-terminal
region of mammalian TAF1; redundant with Bdf1p
RNA polymerase I enhancer binding protein; DNA binding
protein which binds to genes transcribed by both RNA
polymerase I and RNA polymerase II; required for termination
of RNA polymerase I transcription
Decapping enzyme, essential phosphoprotein component of
mRNA decapping complex, plays key role in mRNA decay by
cleaving off the 5' cap to leave the end susceptible to
exonucleolytic degradation; regulated by DEAD box protein
Dhh1p
Transcription factor that binds to a number of promoter regions,
particularly promoters of some genes involved in pheromone
response and cell cycle; potential Cdc28p substrate; expression
is induced in G1 by bound SBF
Nim1p-related protein kinase that regulates the morphogenesis
and septin checkpoints; associates with the assembled septin
filament; required along with Hsl7p for bud neck recruitment,
phosphorylation, and degradation of Swe1p
putative alanine transaminase (glutamyc pyruvic transaminase)
Protein kinase that regulates the G2/M transition by inhibition of
Cdc28p kinase activity; localizes to the nucleus and to the
daughter side of the mother-bud neck; homolog of S. pombe
Wee1p; potential Cdc28p substrate
Essential protein required for sister chromatid cohesion in
mitosis and meiosis; subunit of the cohesin complex; expression
is cell cycle regulated and peaks in S phase
Protein required for the spindle pole body (SPB) duplication,
localized at the central plaque periphery; forms a complex with a
nuclear envelope protein Mps2p and SPB components Spc29p
YMR075W
RCO1
YPL032C
SVL3
YPL153C
RAD53
YJR053W
BFA1
YMR001C
CDC5
YMR032W
HOF1
and Kar1p; required for mitotic functions of Cdc5p
Hypothetical ORF
Protein of unknown function, mutant phenotype suggests a
potential role in vacuolar function; green fluorescent protein
(GFP)-fusion protein localizes to the cell periphery, cytoplasm,
bud, and bud neck
Protein kinase, required for cell-cycle arrest in response to DNA
damage; activated by trans autophosphorylation when
interacting with hyperphosphorylated Rad9p
Component of the GTPase-activating Bfa1p-Bub2p complex
involved in multiple cell cycle checkpoint pathways that control
exit from mitosis
Bud neck-localized, SH3 domain-containing protein required for
cytokinesis; regulates actomyosin ring dynamics and septin
localization; interacts with the formins, Bni1p and Bnr1p, and
with Cyk3p, Vrp1p, and Bni5p
(77) MODULE 89
Genotype regulators
YLR149C-A STM1(0,0) PCD1(0,2) YLR152C ACS2(2,0)
RNH203(0,3) YLR154C-G YLR154C-H TAR1(0,0)
YLR154W-B YLR154W-C YLR154W-E YLR154W-F ASP31(193,529) YLR156C-A YLR156W ASP3-2(193,524)
YLR157C-C YLR157W-A YLR157W-C ASP3-3(193,529)
YLR159C-A YLR159W ASP3-4(193,529) YLR161W
YLR162W YLR162W-A YLR162W- MAS1(3,5) YLR163W-A
YLR164W PUS5(3,1) SEC10(7,11) RPS31(0,11) YLR168C
YLR169W APS1(1,2) YLR171W DPH5(0,5) YLR173W
IDP2(0,3) CBF5(1,2) RFX1(13,11) YLR177W TFS1(1,3)
YLR179C SAM1(0,10) VTA1(4,4)
M12_450041_508029
Module genes
YLR179C
None
YLR151C
PCD1
YIL066C
RNR3
YJL026W
RNR2
(78) MODULE 90
YOR090C
PTC5
Peroxisomal nudix pyrophosphatase with specificity for
coenzyme A and CoA derivatives, may function to remove
potentially toxic oxidized CoA disulfide from peroxisomes to
maintain the capacity for beta-oxidation of fatty acids
Ribonucleotide-diphosphate reductase (RNR), large subunit; the
Ribonucleotide-diphosphate reductase (RNR), small subunit; the
YHR056C
Module genes
YER098W
RSC30
UBP9
YPL083C
SEN54
YOR162C
YRR1
YPR121W
THI22
Ubiquitin-specific protease that cleaves ubiquitin-protein fusions
Subunit of the tRNA splicing endonuclease, which is composed
of Sen2p, Sen15p, Sen34p, and Sen54p
Zn2-Cys6 zinc-finger transcription factor that activates genes
involved in multidrug resistance; paralog of Yrm1p, acting on an
overlapping set of target genes
Protein with similarity to hydroxymethylpyrimidine phosphate
kinases; member of a gene family with THI20 and THI21; not
required for thiamine biosynthesis
YNL105W
YBR178W
YJL150W
YGL088W
(79) MODULE 93
None
None
None
None
YAL017W
PSK1
Genotype regulators
HMG2(4,5) LEU3(6,0) SST2(2,0) RIF2(6,6) FMP27(8,6)
YLR455W YLR456W NBP1(2,5) YLR458W GAB1(1,5)
YLR460C PAU4(1,435)
M12_1042072_1054302
Module genes
YGL157W
YLR438W
YCR105W
None
CAR2
ADH7
YGL263W
COS12
YCR106W
RDS1
YOL165C
AAD15
YCR107W
AAD3
ornithine aminotransferase
NADP(H)-dependent alcohol dehydrogenase; ORF
Regulator of drug sensitivity; transcriptional regulator
(80) MODULE 94
YNL239W
LAP3
YPL002C
SNF8
Aminopeptidase of cysteine protease family, has a DNA binding
activity and acts as bleomycin hydrolase in vitro; transcription is
regulated by galactose via Gal4p
derepression
Genotype regulators
M14_486861_486861
RPL16B(8,0) TOM7(0,3) LAT1(1,0) RNH201(0,0) MSK1(1,0)
MLF3(4,0) IMP4(0,1) MKS1(1,0) APJ1(1,1) NIS1(1,0)
TPM1(0,0) YNL080C
Module genes
YDR089W
None
YCR048W
ARE1
YGL209W
MIG2
YJL052W
YPR157W
YJR009C
TDH1
None
TDH2
YOR383C
FIT3
YKL060C
FBA1
YEL047C
None
YFR009W
GCN20
YBR196C
PGI1
YNL046W
None
YOR230W
WTM1
HXT3
Low affinity glucose transporter of the major facilitator
superfamily, expression is induced in low or high glucose
conditions
Acyl-CoA:sterol acyltransferase, isozyme of Are2p;
endoplasmic reticulum enzyme that contributes the major sterol
esterification activity in the absence of oxygen
Involved in repression, along with Mig1p, of SUC2 (invertase)
expression by high levels of glucose; binds to Mig1p-binding
sites in SUC2 promoter; Protein containing zinc fingers very
similar to zinc fingers in Mig1p
Glyceraldehyde-3-phosphate dehydrogenase 1
glyceraldehyde 3-phosphate dehydrogenase
Mannoprotein that is incorporated into the cell wall via a
glycosylphosphatidylinositol (GPI) anchor, involved in the
retention of siderophore-iron in the cell wall
Fructose 1,6-bisphosphate adolase, required for glycolysis and
gluconeogenesis
uncharged tRNA
Glycolytic enzyme phosphoglucose isomerase, catalyzes the
interconversion of glucose-6-phosphate and fructose-6phosphate; required for cell cycle progression and completion of
the gluconeogenic events of sporulation
(81) MODULE 95
Module genes
YDR345C
(82) MODULE 97
Genotype regulators
RPL14B(43,144) YHL002C-A HSE1(1,3) LAG1(1,4)
MRP4(0,2) YHL005C SHU1(2,2) YHL006W-A STE20(7,2)
YHL008C YAP3(10,400) YHL010C PRS3(0,3) YHL012W
YHL013C YLF2(0,0) RPS20(0,0) YHL015W-A DUR3(0,3)
YHL017W
M8_80014_95469
Module genes
YHL010C
None
YCL055W
KAR4
YJL113W
None
YLR452C
SST2
YHL009C
YAP3
YHL022C
SPO11
Protein involved in desensitization to alpha-factor pheromone;
member of the RGS (regulator of G-protein signalling) family;
GTPase-activating protein
Meiosis-specific protein that initiates meiotic recombination by
catalyzing the formation of double-strand breaks in DNA via a
transesterifcation reaction; required for homologous
chromosome pairing and synaptonemal complex formation
(83) MODULE 99
YFR009W
GCN20
YOL113W
SKM1
YJL005W
CYR1
YPL016W
SWI1
Module genes
YBR044C
YIL022W
TCM62
TIM44
YJR122W
CAF17
YOL166C
None
YOR201C
PET56
YPL140C
MKK2
YHR099W
TRA1
YGL215W
CLG1
YMR316C-A
None
YBR227C
MCX1
YMR316W
DIA1
YFL016C
MDJ1
YLR193C
None
uncharged tRNA
Cla4p
mitochondrial protein; (putative) chaperone
48.8 kDa protein involved in mitochondrial protein import
proteins
Ribose methyltransferase that modifies a functionally critical,
conserved nucleotide in mitochondrial 21S rRNA
Member of MAP kinase pathway involving PKC1, BCK1, and
SLT2. Shows functional redundancy with MKK1; protein kinase
Histone acetyltransferase component, putative ortholog of
human TRRAP which is an essential cofactor of c-Myc
cyclin-like protein that interacts with Pho85p in affinity
chromatography; cyclin-like protein that interacts with Pho85
Mitochondrial ATP-binding protein, possibly a mitochondrial
chaperone with non-proteolytic function; similar to bacterial
ClpX proteins
Protein of unknown function, involved in invasive and
pseudohyphal growth; green fluorescent protein (GFP)-fusion
protein localizes to the cytoplasm in a punctate pattern
Protein involved in folding of mitochondrially synthesized
proteins in the mitochondrial matrix; localizes to the
mitochondrial inner membrane; member of the DnaJ family of
molecular chaperones
YHR217C
None
YDR393W
SHE9
YPR047W
MSF1
Mitochondrial inner membrane protein required for normal
mitochondrial morphology, may be involved in fission of the
inner membrane; forms a homo-oligomeric complex
Mitochondrial phenylalanyl-tRNA synthetase alpha subunit,
active as a monomer, unlike the cytoplasmic subunit which is
active as a dimer complexed to a beta subunit dimer; similar to
the alpha subunit of E. coli phenylalanyl-tRNA synthetase
(84) MODULE 100
YJL098W
SAP185
YIL101C
XBP1
Module genes
YPL262W
FUM1
YGL158W
RCK1
YGR279C
SCW4
YPL275W
None
YDR247W
VHS1
YDR529C
YPL276W
YPR156C
QCR7
None
TPO3
YOR388C
FDH1
YKL123W
YAR053W
YMR304C-A
None
None
None
YPR193C
HPA2
Fumarase, converts fumaric acid to L-malic acid in the TCA
cycle; cytosolic and mitochondrial localization determined by
the N-terminal mitochondrial targeting sequence and protein
conformation
Cell wall protein with similarity to glucanases; scw4 scw10
double mutants exhibit defects in mating
Gene whose overexpression suppresses the synthetic lethality of
the hal3 sit4 double mutation
ubiquinol-cytochrome c oxidoreductase subunit 7 (14 kDa)
Polyamine transport protein
NAD(+)-dependent formate dehydrogenase, may protect cells
from exogenous formate
Tetrameric histone acetyltransferase with similarity to Gcn5p,
Hat1p, Elp3p, and Hpa3p; acetylates histones H3 and H4 in vitro
and exhibits autoacetylation activity
(85) MODULE 101
Genotype regulators
EDC3(0,0) YEL016C PMP2(0,0) GTT3(1,0) YEL018C-A
EAF5(0,0) MMS21(1,0) YEL020C YEL020C-B TIM9(0,3)
URA3(222,250) GEA2(5,1) YEL023C RIP1(1,5) YEL025C
SNU13(0,1) CUP5(0,0)
M5_109310_117705
Module genes
YIL171W
YEL021W
None
URA3
orotidine-5'-phosphate decarboxylase
YMR011W
HXT2
YEL038W
UTR4
superfamily, expression is induced by low levels of glucose and
repressed by high levels of glucose
Protein of unknown function, found in both the cytoplasm and
nucleus
(86) MODULE 102
Genotype regulators
YMR310C GLC8(0,3) ELP6(1,3) TGL3(1,5) PRE5(0,5)
YMR315W YMR315W-A YMR316C-A YMR316C-B
DIA1(1,4) YMR317W ADH6(0,8) FET4(1,8) YMR320W
YMR321C SNO4(1,20) ERR3 YMR324C YMR325W
YMR326C
M13_905780_922268
Module genes
YMR319C
(87) MODULE 108
FET4
YGL166W
CUP2
YIR017C
MET28
Low-affinity Fe(II) transporter of the plasma membrane
Module genes
YJL065C
DLS1
YJR071W
YDL009C
None
None
YBR278W
DPB3
YGR242W
None
YCR063W
BUD31
Subunit of ISW2/yCHRAC chromatin accessibility complex
along with Itc1p, Isw2p, and Dpb4p; involved in inheritance of
telomeric silencing
Third-largest subunit of DNA polymerase II (DNA polymerase
epsilon), required to maintain fidelity of chromosomal
replication and also for inheritance of telomeric silencing;
mRNA abundance peaks at the G1/S boundary of the cell cycle
(88) MODULE 109
YIL101C
XBP1
YPR070W
MED1
Module genes
YIR020W-B
None
YOR032C
HMS1
YOR107W
RGS2
regulation
C2H2 zinc-finger protein with similarity to myc-family
transcription factors; overexpression confers hyperfilamentous
growth and suppresses the pseudohyphal filamentation defect of
a diploid mep1 mep2 homozygous null mutant
Negative regulator of glucose-induced cAMP signaling; directly
YGR108W
CLB1
YBR072W
HSP26
YER103W
SSA4
YHL028W
WSC4
YIL059C
YKL051W
None
SFK1
YER038C
KRE29
YIL119C
RPI1
YNL202W
SPS19
activates the GTPase activity of the heterotrimeric G protein
alpha subunit Gpa2p
Small heat shock protein with chaperone activity that is
regulated by a heat induced transition from an inactive
oligomeric (24-mer) complex to an active dimer; induced by
heat, upon entry into stationary phase, and during sporulation
member of 70 kDa heat shock protein family
cell wall integrity and stress response component 4; Putative
integral membrane protein containing novel cysteine motif.
Similarity to SLG1 (WSC1), WSC2 and WSC3
Suppressor of PI Four Kinase
Essential protein of unknown function; heterozygous mutant
shows haploinsufficiency in K1 killer toxin resistance
late sporulation specific gene which may function during spore
wall formation; peroxisomal 2,4-dienoyl-CoA reductase
(89) MODULE 111
YDL064W
UBC9
(APCC)
Genotype regulators
NNF1(0,0) YJR112W-A RSM7(0,0) SRF2(1,0) YJR115W
YJR116W STE24(2,2) ILM1(1,0) YJR119C YJR120W
ATP2(1,0) CAF17(0,2) RPS5(0,1) YJR124C ENT3(0,0)
M10_646911_646911
Module genes
YJR095W
SFC1
YJR131W
YFL061W
MNS1
DDI2
YNL333W
SNZ2
YFL060C
SNO3
YFL059W
SNZ3
Mitochondrial succinate-fumarate transporter, transports
succinate into and fumarate out of the mitochondrion; required
for ethanol and acetate utilization
specific alpha-mannosidase
Hypothetical ORF
Snooze: stationary phase-induced gene family; member of the
stationary phase-induced gene family
Protein of unknown function, nearly identical to Sno2p;
expression is induced before the diauxic shift and also in the
absence of thiamin
Snooze: stationary phase-induced gene family; member of the
stationary phase-induced gene family
(90) MODULE 117
Genotype regulators
M14_314883_330368
YNL158W ASI2(0,0) YGP1(3,1) CBK1(3,1) RPL42A(1,2)
YNL162W-A RIA1(1,3) IBD2(0,0) YNL165W BNI5(133,2)
SKO1(1,0) FMP41(0,1) PSD1(0,0) YNL170W YNL171C
APC1(4,1) MDG1(1,1) YNL174W NOP13(1,3) YNL176C
Module genes
YNL179C
SRF6
conserved in closely related Saccharomyces species; deletion in
cyr1 mutant results in loss of stress resistance
(91) MODULE 119
Genotype regulators
PTM1(17,1) NFU1(0,1) VPS24(1,0) SPC42(1,2) PHD1(1,1)
YKL044W PRI2(1,6) DCW1(0,6) YKL047W ELM1(0,0)
CSE4(0,0)
M11_354466_354466
Module genes
YKL043W
PHD1
protein similar to StuA of Aspergillus nidulans; putative
(92) MODULE 121
Genotype regulators
NUC1(1,2) CBP1(6,3) PEX2(1,6) YJL211C OPT1(3,6)
YJL213W HXT8(93,12) YJL215C YJL216C YJL217W
YJL218W HXT9(12,50) YJL220W FSP2(4,32) VTH2(323,435)
M10_22213_34098
Module genes
YJL221C
FSP2
YJL218W
(93) MODULE 122
Genotype regulators
None
Protein of unknown function, expression is induced during
nitrogen limitation
GYP5(1,2) RPL36B(5,6) ICY2(1,12) YPL250W-A YPL251W
YAH1(1,2) VIK1(4,3) HFI1(1,3) BBP1(0,4) CLN2(1,3)
YPL257W
M16_70847_70853
Module genes
YPL252C
YAH1
Iron-sulfur protein of the mitochondrial matrix, homologous to
human adrenodoxin; involved in heme a biosynthesis
(94) MODULE 124
Genotype regulators
DEG1(3,5) SPB4(2,5) YFL002W-A MSH4(5,187) VTC2(2,4)
SEC4(1,3) YFL006W BLM3(10,3) LOC1(0,49) NIC96(2,3)
YPI1(0,3) RPN11(0,3) SAD1(5,3) YFR006W YFR007W
FAR7(2,1) GCN20(1,13) YFR009W-A UBP6(0,2) YFR010WA YFR011C YFR012W YFR012W-A
M6_134096_161065
Module genes
YFL010C
WWM1
YFL011W-A
(95) MODULE 125
Genotype regulators
None
UBC11(0,0) RPA43(1,3) RPA190(2,3) YOR342C YOR343C
TYE7(0,0)
M15_968429_968429
Module genes
YOR345C
WW domain containing protein interacting with Metacaspase
(MCA1)
None
YOR346W
REV1
Deoxycytidyl transferase, forms a complex with the subunits of
DNA polymerase zeta, Rev3p and Rev7p; involved in repair of
abasic sites in damaged DNA
(96) MODULE 126
Genotype regulators
YLL014W
M12_131338_131338
Module genes
YGR144W
THI4
Protein required for thiamine biosynthesis and for mitochondrial
genome stability
(97) MODULE 128
Genotype regulators
PPZ2(1,0) YDR437W YDR438W LRS4(0,0) DOT1(2,10)
APT2(1,6) YDR442W SSN2(4,1) YDR444W YDR445C
ECM11(0,156)
M4_1344550_1344670
Module genes
YDR451C
YHP1
YDR441C
APT2
acts as a repressor at early cell cycle boxes (ECBs) to restrict
their activity to the M/G1 phase of the cell cycle.
Apparent pseudogene, not transcribed or translated under normal
conditions; encodes a protein with similarity to adenine
phosphoribosyltransferase, but artificially expressed protein
exhibits no enzymatic activity
(98) MODULE 130
Genotype regulators
MYO1(16,4) MAS2(0,2) THR1(1,2) PPA1(0,1) RPN1(3,8)
DAP2(3,22) YHR028W-A YHR029C SLT2(0,4) RRM3(3,12)
YHR032C-A YHR032W YHR032W-A YHR033W PIH1(4,6)
YHR035W YHR036W PUT2(2,1) RRF1(2,10) MSC7(0,7)
M8_161987_176994
Module genes
YHR022C
(99) MODULE 131
Genotype regulators
None
YOL008W MDM12(1,3) RCL1(0,2) PLB3(0,1) HTZ1(0,1)
HRD1(1,2) YOL013W-A YOL013W-B YOL014W YOL015W
CMK2(1,1) ESC8(5,2) TLG2(0,2) YOL019W YOL019W-A
TAT2(0,2) DIS3(2,2) YOL022C
M15_290670_301077
Module genes
YOL019W
(100) MODULE 132
Genotype regulators
None
ECM15(0,22) HTB2(0,13) HTA2(0,13) UTP20(35,140)
PDR3(3,1) YBL005W-A YBL005W-B LDB7(2,1) YBL006WA SLA1(9,2) HIR1(3,0) YBL008W-A YBL009W NTH2(7,4)
RER2(1,2) COQ1(1,2) GPI18 RCR1(2,2) UGA2(0,5) DSF2(9,8)
FLR1(5,15) HHF1(0,331)
M2_216978_246135
Module genes
YBL005W
PDR3
Transcriptional activator of the pleiotropic drug resistance
network, regulates expression of ATP-binding cassette (ABC)
transporters through binding to cis-acting sites known as PDREs
(PDR responsive elements)
(101) MODULE 133
Genotype regulators
GLN3(4,0) YEN1(4,1) MXR1(0,2) SAH1(0,1) ERG28(0,3)
MEI4(95,2) ACA1(9,27) SPO73(1,14) YER046W-A SAP1(7,5)
CAJ1(0,8) YER048W-A YER049W
M5_240105_244117
Module genes
YER047C
SAP1
Putative ATPase of the AAA family, interacts with the Sin1p
transcriptional repressor in the two-hybrid system
(102) MODULE 134
Genotype regulators
RPS6A(2,377) GLR1(3,4) SSU1(6,10) NOG1(0,3) SEC62(0,3)
YPL095C ERI1(1,0) PNG1(0,0) MSY1(0,0) YPL098C
FMP14(0,0) ATG21(1,0) ELP4(0,2) YPL102C FMP30(0,2)
M16_368086_368296
Module genes
YPL091W
GLR1
Cytosolic and mitochondrial glutathione oxidoreductase,
converts oxidized glutathione to reduced glutathione
(103) MODULE 135
Genotype regulators
PBI2(0,6) PUB1(1,20) YNL017C YNL018C YNL019C
ARK1(3,10) HDA1(2,3) YNL022C FAP1(10,9) YNL024C
YNL024C-A SSN8(1,8) SAM50(3,2) CRZ1(3,1) YNL028W
KTR5(5,1) HHF2(0,7) HHT2(0,7) SIW14(1,13) YNL033W
YNL034W YNL035C
M14_571885_595885
Module genes
YNL019C
(104) MODULE 136
Genotype regulators
None
TIP1(6,9) BAP2(3,7) TAT1(3,3) YBR070C YBR071W
YBR072C-A HSP26(2,26) RDH54(5,2) YBR074W YBR075W
YBR076C-A ECM8(195,23) EGO3 ECM33(64,7)
RPG1(551,164)
M2_380926_388862
Module genes
YBR066C
NRG2
Transcriptional repressor that mediates glucose repression and
negatively regulates filamentous growth; has similarity to Nrg1p
(105) MODULE 137
Genotype regulators
CYC1(0,8) UTR1(2,1) ISY1(0,1) OSM1(0,1) RAD7(0,2)
BFA1(1,3) YJR054W HIT1(2,350) YJR056C CDC8(1,119)
APS2(0,5) PTK2(89,5) CBF1(2,7) YJR061W NTA1(2,5)
RPA12(0,5) CCT5(0,0)
M10_535311_548177
Module genes
YJR060W
CBF1
Helix-loop-helix protein that binds the motif CACRTG (R=A or
G), which is present at several sites including MET gene
promoters and centromere DNA element I (CDEI); required for
nucleosome positioning at this motif; targets Isw1p to DNA
(106) MODULE 138
Genotype regulators
VMA8(0,5) AFG1(139,5) MAK10(1,5) YEL053W-A
RPL12A(0,7) POL5(9,7) HAT2(2,16) YEL057C PCM1(4,5)
SOM1(0,5) YEL059W PRB1(4,2) CIN8(4,4) NPR2(2,6)
M5_44605_48845
Module genes
YEL057C
(107) MODULE 139
Genotype regulators
None
YPR074W-A OPY2(1,1) YPR076W YPR077C YPR078C
MRL1(0,2) TEF1(0,318) GRS2(0,0) DIB1(1,0) MDM36(0,0)
YPR084W YPR085C SUA7(1,2) VPS69(5,0) SRP54(196,0)
YPR089W YPR090W YPR091C YPR092W ASR1(1,14)
RDS3(0,14)
M16_704388_711614
Module genes
YPR085C
(108) MODULE 140
Genotype regulators
None
RTS2(2,1) BUD21(1,1) ATX2(0,1) DIA2(11,1) STC2(0,3)
YOR082C WHI5(0,4) YOR084W OST3(0,2) TCB1(547,473)
YVC1(2,7) YOR088W VPS21(0,5)
M15_481586_481586
Module genes
YOR081C
STC2
Protein of unknown function, localizes to lipid particles;
(109) MODULE 141
Genotype regulators
YOL008W MDM12(1,3) RCL1(0,2) PLB3(0,1) HTZ1(0,1)
HRD1(1,2) YOL013W-A YOL013W-B YOL014W YOL015W
CMK2(1,1) ESC8(5,2) TLG2(0,2) YOL019W YOL019W-A
TAT2(0,2) DIS3(2,2) YOL022C
M15_290670_301077
Module genes
YOL014W
(110) MODULE 142
Genotype regulators
None
YGL250W HFM1(22,0) RTG2(1,1) HXK2(0,11) FZF1(2,3)
ZRT1(27,1) ADH4(6,1) MNT2(11,1) YGL258W YGL258W-A
YPS5(0,2) YGL260W YGL261C YGL262W COS12(141,872)
M7_3714_23129
Module genes
YGL262W
(111) MODULE 143
Genotype regulators
None
RPL19A(1,370) YBR085C-A AAC3(1,15) IST2(7,8) RFC5(0,8)
POL30(0,0) NHP6B(1,2) YBR089W YBR090C YBR090C-A
MRS5(0,6) PHO3(2,5) PHO5(1,10) YBR094W RXT2(3,1)
YBR096W
M2_424450_427683
Module genes
YBR103W
SIF2
Sir4p-Interacting Factor; 535 amino acid protein containing 4
WD-40 repeats and a nuclear localization signal
(112) MODULE 144
Genotype regulators
CDC40(0,0) ESF1(0,407) YDR366C YDR367W YPR1(0,0)
XRS2(2,0) YDR370C YDR371C-A CTS2(3,0) VPS74(0,1)
FRQ1(0,1)
M4_1213416_1213416
Module genes
YDR367W
(113) MODULE 145
YOR090C
Module genes
YLR282C
(114) MODULE 146
Genotype regulators
None
PTC5
None
DCP2(10,13) NCS2(2,2) YNL120C TOM70(1,2) YNL122C
YNL123W NAF1(5,3) ESBP6(7,3) SPC98(1,0) FAR11(1,1)
TEP1(1,0) NRK1(1,0) CPT1(18,1) YNL130C-A TOM22(0,0)
KRE33(3,3) FYV6(1,3) YNL134C FPR1(0,2) EAF7(3,1)
NAM9(1,1) SRV2(3,3) RCP10(2,0) RLR1(9,0)
M14_371953_394161
Module genes
YNL134C
(115) MODULE 147
Genotype regulators
None
MDS3(20,6) YIP4(0,3) YGL199C EMP24(0,3) MCM6(4,9)
ARO8(1,144) KEX1(260,309) YGL204C POX1(7,6)
CHC1(6,6) SPT16(2,10) SIP2(3,0) MIG2(1,10) YPT32(0,1)
YGL210W-A NCS6(1,1) VAM7(3,0) SKI8(1,0) YGL214W
CLG1(14,3)
M7_98231_117900
Module genes
YGL201C
MCM6
Protein involved in DNA replication; component of the Mcm2-7
hexameric complex that binds chromatin as a part of the prereplicative complex
(116) MODULE 148
Genotype regulators
RAD16(2,9) LYS2(372,217) YBR116C TKL2(0,22)
TEF2(0,20) MUD1(8,5) CBP6(0,4) GRS1(3,3) YBR121C-A
MRPL36(0,5) TFC1(3,4) YBR124W PTC4(0,9) TPS1(0,1)
YBR126W-A YBR126W-B VMA2(0,0) ATG14(0,0)
OPY1(0,2) SHE3(1,0)
M2_477206_486640
Module genes
YBR115C
(117) MODULE 149
Genotype regulators
LYS2
Alpha aminoadipate reductase, catalyzes the reduction of alphaaminoadipate to alpha-aminoadipate 6-semialdehyde, which is
the fifth step in biosynthesis of lysine; activation requires
posttranslational phosphopantetheinylation by Lys5p
PBI2(0,6) PUB1(1,20) YNL017C YNL018C YNL019C
ARK1(3,10) HDA1(2,3) YNL022C FAP1(10,9) YNL024C
YNL024C-A SSN8(1,8) SAM50(3,2) CRZ1(3,1) YNL028W
KTR5(5,1) HHF2(0,7) HHT2(0,7) SIW14(1,13) YNL033W
YNL034W YNL035C
M14_571885_595885
Module genes
YNL040W
(118) MODULE 150
Genotype regulators
None
SUI2(0,2) YJR008W TDH2(0,8) SPC1(0,1) MET3(0,24)
YJR011C YJR012C GPI14(2,4) RBF22 YJR015W ILV3(1,3)
ESS1(1,0) YJR018W TES1(0,1) YJR020W REC107(108,2)
LSM8(0,2) YJR023C YJR024C BNA1(1,78) YJR026W
M10_461201_464261
Module genes
YJR010C-A
SPC1
Subunit of the signal peptidase complex (SPC), which cleaves
the signal sequence from proteins targeted to the endoplasmic
reticulum (ER), homolog of the SPC12 subunit of mammalian
signal peptidase complex
(119) MODULE 151
Genotype regulators
RME1(1,0) YGR045C YGR046W TFC4(1,1) UFD1(0,1)
SCM4(0,3) YGR050C YGR051C FMP48(0,9) YGR053C
YGR054W MUP1(0,6)
M7_592983_592983
Module genes
YGR050C
(120) MODULE 152
Genotype regulators
None
YLL014W
M12_131338_131338
Module genes
YLL010C
PSR1
Plasma membrane associated protein phosphatase involved in
the general stress response; required along with binding partner
Whi2p for full activation of STRE-mediated gene expression,
possibly through dephosphorylation of Msn2p
(121) MODULE 153
Genotype regulators
HEK2(3,6) RIB1(0,6) STU1(4,1) POL12(5,2) YBL036C
APL3(4,2) MRPL16(2,21) URA7(0,21) YBL039C-A
YBL039W-A ERD2(7,5) PRE7(23,9) FUI1(5,9) ECM13(0,2)
YBL044W COR1(2,5) YBL046W EDE1(5,2) YBL048W
MOH1(0,4) SEC17(10,4) PIN4(6,4)
M2_133737_151686
Module genes
YBL044W
(122) MODULE 154
Genotype regulators
M2_745748_754059
None
FMP51(0,0) SHM1(0,0) YPT10(0,0) TSC10(1,0) SLM6
REI1(3,0) MRPL37(1,0) FMP21(0,3) YBR270C YBR271W
HSM3(4,2) UBX7(5,1) CHK1(1,1) RIF1(27,6) PPS1(4,0)
YBR277C DPB3(1,0) PAF1(0,0) YBR280C
Module genes
YBR274W
CHK1
(123) MODULE 155
Genotype regulators
RAD24(3,1) GRX4(3,2) TMT1(2,1) YER175W-A
ECM32(5,17) BMH1(0,3) PDA1(0,1) DMC1(44,9) ISC10(6,4)
SLO1(0,9) YER181C FMP10(2,4) FAU1(1,31) YER184C
M5_546664_549142
Module genes
YER187W
(124) MODULE 156
Genotype regulators
None
YNL158W ASI2(0,0) YGP1(3,1) CBK1(3,1) RPL42A(1,2)
YNL162W-A RIA1(1,3) IBD2(0,0) YNL165W BNI5(133,2)
SKO1(1,0) FMP41(0,1) PSD1(0,0) YNL170W YNL171C
APC1(4,1) MDG1(1,1) YNL174W NOP13(1,3) YNL176C
M14_314883_330368
Module genes
YNL180C
RHO5
Non-essential small GTPase of the Rho/Rac subfamily of Raslike proteins, likely involved in protein kinase C (Pkc1p)dependent signal transduction pathway that controls cell
integrity
(125) MODULE 157
Genotype regulators
AQY1(17,26) HPA2(1,8) OPT2(25,180) YPR195C YPR196W
YPR197C SGE1(0,0) ARR1(0,0) ARR2(0,0) ARR3(4,0)
M16_932310_932538
Module genes
YPR201W
ARR3
Arsenite transporter of the plasma membrane, required for
resistance to arsenic compounds; transcription is activated by
Arr1p in the presence of arsenite
(126) MODULE 158
Genotype regulators
ALG6(3,0) YSP3(2,0) YOR004W DNL4(2,0) YOR006C
SGT2(0,7) SLG1(0,0) YOR008C-A YOR008W-B TIR4(5,2)
TIR2(0,1) AUS1(5,8) YOR011W-A YOR012W YOR013W
RTS1(2,11)
M15_338018_348934
Module genes
YOR019W
(127) MODULE 159
Genotype regulators
None
YOL036W YOL037C YOL038C-A PRE6(0,2) RPP2A(0,3)
RPS15(0,3) NOP12(4,1) NGL1(1,1) NTG2(4,1) PEX15(230,1)
PSK2(3,4) YOL046C YOL047C YOL048C GSH2(0,3)
M15_248746_248746
Module genes
YOL043C
(128) MODULE 160
NTG2
DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase
involved in base excision repair, localizes to the nucleus
Genotype regulators
PEP12(0,1) CYC2(2,1) HIR2(2,1) CKB2(0,1) GLO4(0,1)
SRF5(2,0) CUE5(3,3) WHI2(5,7) YOR044W TOM6(0,5)
DBP5(1,12) STD1(4,17) RAT1(3,31) RSB1(1,12) YOR050C
YOR051C YOR052C YOR053W VHS3(12,4) YOR055W
NOB1(0,3) SGT1(4,3) ASE1(5,11) YOR059C YOR060C
CKA2(0,6) YOR062C RPL3(0,7) YNG1(1,1) CYT1(0,1)
M15_409775_439041
Module genes
YOR049C
RSB1
Suppressor of sphingoid long chain base (LCB) sensitivity of an
LCB-lyase mutation; putative integral membrane transporter or
flippase that may transport LCBs from the cytoplasmic side
toward the extracytoplasmic side of the membrane
(129) MODULE 161
Genotype regulators
RMD1(0,1) NHP10(0,1) MCD1(5,22) ATP16(0,2) MED2(8,2)
PTC1(0,4) RPT2(0,382) APC11(1,8) YDL009C YDL010W
YDL011C YDL012C HEX3(0,1) NOP1(0,3) TSC13(1,3)
YDL016C CDC7(2,0) ERP3(39,0) NTH1(0,4) YRB1(0,4)
RCR2(0,5) YDR003W-A RAD57(1,3) MAF1(2,2) SOK1(0,4)
TRP1(1,4) YDR008C GAL3(1,4) YDR010C SNQ2(277,9)
RPL4B(0,2) PSF1(0,0) RAD61(51,0) YDR015C DAD1(0,0)
KCS1(2,2) YDR018C GCV1(0,5) YDR020C FAL1(2,0)
M4_432483_478080
Module genes
YDL012C
(130) MODULE 162
Genotype regulators
None
PTM1(17,1) NFU1(0,1) VPS24(1,0) SPC42(1,2) PHD1(1,1)
YKL044W PRI2(1,6) DCW1(0,6) YKL047W ELM1(0,0)
CSE4(0,0)
M11_354466_354466
Module genes
YKL044W
(131) MODULE 163
Genotype regulators
None
YML053C CYB2(0,2) YML054C-A SPC2(0,3) IMD4(59,289)
YML057C-A CMP2(1,7) SML1(0,1) HUG1(0,0) NTE1
OGG1(0,1) PIF1(2,1) MFT1(0,1) RPS1B(0,8) TEM1(0,8)
ORC1(2,9) SMA2(2,9) ERV41(12,2)
M13_149075_159533
Module genes
YML066C
(132) MODULE 164
Genotype regulators
M8_193175_209245
Module genes
SMA2
Spore Membrane Assembly
RRF1(2,10) MSC7(0,7) VMA10(1,3) YHR039C-B BCD1(0,5)
SRB2(6,3) NCP1(4,3) DOG2(11,284) DOG1(11,0) YHR045W
INM1(1,6) AAP1'(0,0) YHR048W YHR049C-A FSH1(0,0)
SMF2(49,1) YHR050W-A COX6(0,0) CIC1(5,2) YHR052W-A
CUP1-1(0,7) YHR054C YHR054W-A CUP1-2(0,7)
RSC30(4,1) YHR056W-A CPR2(0,3)
YHR043C
DOG2
2-deoxyglucose-6-phosphate phosphatase, member of a family
of low molecular weight phosphatases, similar to Dog1p,
induced by oxidative and osmotic stress, confers 2-deoxyglucose
resistance when overexpressed
(133) MODULE 165
Genotype regulators
FSH3(1,9) PLP2(4,1) YOR282W YOR283W HUA2(6,1)
YOR285W FMP31(1,4) YOR287C MPD1(1,0) YOR289W
SNF2(6,29) YOR291W YOR292C YOR293C-A RPS10A(17,1)
RRS1(0,0) UAF30(0,0) YOR296W TIM18(1,1) MBF1(0,0)
YOR298W BUD7(0,1) YOR300W RAX1(2,1) YOR302W
CPA1(2,0) YOR304C-A ISW2(4,0) YOR305W MCH5(8,9)
M15_854265_880786
Module genes
YOR285W
(134) MODULE 166
Genotype regulators
None
YDR417C RPL12B(0,346) RAD30(0,2) HKR1(861,636)
ARO80(1,0) SIP1(3,1) CAD1(3,0) DYN2(16,0) SNX41(1,0)
YDR426C RPN9(0,2) YDR428C TIF35(0,0) CYM1(0,0)
M4_1310380_1318073
Module genes
YDR423C
CAD1
Transcriptional activator involved in resistance to 1,10phenanthroline; member of yeast Jun-family of transcription
factors related to mammalian c-jun; basic leucine zipper
(135) MODULE 167
Genotype regulators
YLR342W-A GAS2(11,6) RPL26A(6,480) YLR345W
YLR346C KAP95(1,2) YLR347W-A DIC1(0,10) YLR349W
ORM2(1,10) NIT3(1,21) YLR352W
M12_824230_824230
Module genes
YLR343W
(136) MODULE 168
Genotype regulators
GAS2
YML003W GLO1(3,12) TRM12(4,5) GIS4(3,4) YML007C-A
YAP1(3,7) ERG6(1,1) MRPL39(0,5) YML009C-A YML009WB SPT5(7,4) YML010W-A YML010C-B YML010W-B
YML011C YML012C-A ERV25(1,0) SEL1(4,0) YML013C-A
TRM9(91,0) TAF11(1,0) PPZ1(1,9) PSP2(6,10)
M13_245457_255564
Module genes
YMR006C
(137) MODULE 169
Genotype regulators
M7_98231_117900
Module genes
Putative 1,3-beta-glucanosyltransferase, has similarity to Gas1p
PLB2
Phospholipase B 2; lysophospholipase/phospholipase B
MDS3(20,6) YIP4(0,3) YGL199C EMP24(0,3) MCM6(4,9)
ARO8(1,144) KEX1(260,309) YGL204C POX1(7,6)
CHC1(6,6) SPT16(2,10) SIP2(3,0) MIG2(1,10) YPT32(0,1)
YGL210W-A NCS6(1,1) VAM7(3,0) SKI8(1,0) YGL214W
CLG1(14,3)
YGL204C
(138) MODULE 170
Genotype regulators
None
PET130(2,2) APS3(7,5) RRN7(0,1) YJL026C-A RNR2(1,2)
YJL027C YJL028W VPS53(2,8) MAD2(0,2) BET4(2,2)
YJL032W HCA4(4,1) KAR2(0,2) TAD2(4,2) SNX4(1,18)
YJL037W YJL038C NUP192(3,22) NSP1(48,118)
M10_374040_387893
Module genes
YJL035C
(139) MODULE 171
Genotype regulators
TAD2
HPA3(1,9) YEL067C YEL068C HXT13(4,11) DSF1(0,31)
DLD3(1,7) RMD6(1,14) YEL073C YEL074W YEL075C
YEL075W-A YEL076C YEL076C-A YEL076W-C YEL077C
YEL077W-A
M5_6335_17399
Module genes
YEL073C
(140) MODULE 172
Genotype regulators
tRNA-specific adenosine-34 deaminase subunit Tad2p
None
YDL157C YDL158C YDL159C-B STE7(1,1) YDL159W-A
DHH1(0,1) YDL160C-A ENT1(0,3) YDL162C YDL163W
CDC9(1,3) CDC36(0,6) FAP7(0,6) NRP1(128,0) SFA1(2,12)
UGX2(6,13) UGA3(3,6) GLT1(5,6)
M4_161196_165032
Module genes
YDL168W
SFA1
Long-chain alcohol dehydrogenase (glutathione-dependent
formaldehyde dehydrogenase)
(141) MODULE 173
Genotype regulators
SGS1(4,3) SPG5(5,3) GYL1(1,10) YMR193C-A MRPL24(1,2)
YMR194C-A YMR194C-B RPL36A(5,2) ICY1(0,1)
YMR196W VTI1(0,2)
M13_649250_649253
Module genes
YMR193C-A
(142) MODULE 174
Genotype regulators
None
CDC13(11,3) YDL221W FMP45(0,3) HBT1(485,1)
WHI4(370,467) SHS1(276,0) GCS1(130,0) HO(573,520)
YDL228C SSB1(0,0) PTP1(2,2) BRE4(2,2) OST4(0,0)
YDL233W
M4_45364_54225
Module genes
YDL231C
(143) MODULE 175
Genotype regulators
M11_522777_522777
BRE4
Zinc finger protein containing five transmembrane domains; null
mutant exhibits strongly fragmented vacuoles and sensitivity to
brefeldin A, a drug which is known to affect intracellular
transport
GAP1(1,43) YKR040C YKR041W UTH1(7,0) YKR043C
UIP5(4,0) YKR045C PET10(0,10) YKR047W NAP1(2,0)
FMP46(0,9) TRK2(109,7) YKR051W MRS4(1,5)
Module genes
YKR039W
GAP1
General amino acid permease; localization to the plasma
membrane is regulated by nitrogen source
(144) MODULE 176
Genotype regulators
YDR524C-A YDR524C-B YDR524W-A API2(1,0) SNA2(0,3)
YDR526C RBA50(7,3) HLR1(63,10) QCR7(0,2) APA2(0,4)
YDR531W YDR532C HSP31(1,13) FIT1(32,68) YDR535C
STL1(2,7) YDR537C PAD1(2,11) YDR539W
M4_1499294_1507292
Module genes
YDR539W
(145) MODULE 177
Genotype regulators
None
YLR046C YLR047C RPS0B(30,9) YLR049C YLR050C
YLR051C IES3(2,2) YLR053C OSW2(8,3) SPT8(8,3)
ERG3(2,12) YLR057W SHM2(0,4) REX2(3,2) FRS1(2,2)
RPL22A(4,7) BUD28(0,0) YLR063W YLR064W YLR065C
SPC3(0,2)
M12_247886_257512
Module genes
YLR049C
(146) MODULE 178
Genotype regulators
None
GYP5(1,2) RPL36B(5,6) ICY2(1,12) YPL250W-A YPL251W
YAH1(1,2) VIK1(4,3) HFI1(1,3) BBP1(0,4) CLN2(1,3)
YPL257W
M16_70847_70853
Module genes
YPL251W
(147) MODULE 179
Genotype regulators
None
YVH1(2,4) DAL1(2,2) DAL4(2,2) DAL2(1,4) DCG1(3,3)
YIR030W-A DAL7(1,2) DAL3(2,4) MGA2(15,4) LYS1(0,1)
YIR035C YIR036C YIR036W-A HYR1(0,3) GTT1(1,20)
M9_415311_420076
Module genes
YIR039C
(148) MODULE 180
Genotype regulators
YPS6
Putative GPI-anchored aspartic protease
YML007C-A ERG6(1,1) MRPL39(0,5) YML009C-A
YML009W-B SPT5(7,4) YML010W-A YML010C-B
YML010W-B YML011C YML012C-A ERV25(1,0) SEL1(4,0)
YML013C-A TRM9(91,0) TAF11(1,0) PPZ1(1,9) PSP2(6,10)
YML018C OST6(2,0) YML020W UNG1(1,5) APT1(1,0)
YML023C RPS17A(1,13) YML6(10,13) RPS18B(16,5)
YOX1(0,5) TSA1(0,0) USA1(0,1)
M13_227254_243624
Module genes
YML016C
PPZ1
Serine/threonine protein phosphatase Z, isoform of Ppz2p;
involved in regulation of potassium transport, which affects
osmotic stability, cell cycle progression, and halotolerance
(149) MODULE 181
Genotype regulators
THS1(2,4) AIR1(3,4) YIL080W YIL082W YIL082W-A
YIL083C SDS3(1,4) KTR7(3,2) YIL086C YIL087C AVT7(3,3)
YIL089W YIL090W YIL091C YIL092W RSM25(0,5)
LYS12(0,2) PRK1(1,9) YIL096C FYV10(1,1)
M9_190794_205191
Module genes
YIL089W
(150) MODULE 182
Genotype regulators
None
YPL176C CUP9(0,2) CBC2(1,339) PPQ1(1,0) TCO89(2,1)
CTI6(0,7) YPL182C YPL183C YPL183W-A YPL184C
YPL185W UIP4(1,1) MF(ALPHA)1(21,1) POS5(1,1)
YPL189C-A GUP2(1,4) NAB3(1,1) YPL191C PRM3(2,3)
RSA1(0,0) DDC1(2,0) APL5(0,1) OXR1(0,1) YPL197C
RPL7B(35,181)
M16_182953_207356
Module genes
YPL189W
GUP2
Multimembrane-spanning protein and putative glycerol
transporter that is essential for proton symport of glycerol;
Gup1p homolog
(151) MODULE 183
Genotype regulators
ACS1(2,7) PEX22(3,3) YAL056C-A GPB2(10,6) CNE1(9,5)
YAL058C-A YAL059C-A ECM1(4,2) BDH1(6,5) YAL061W
GDH3(0,50) FLO9(880,506) YAL063C-A YAL064C-A
YAL064W YAL064W-B YAL065C YAL066W
SEO1(370,503) YAL067W-A YAL068C YAL068W-A
YAL069W
M1_1_37068
Module genes
YAL064C-A
(152) MODULE 184
Genotype regulators
None
HUL4(6,3) YJR037W YJR038C YJR039W GEF1(5,5)
URB2(8,4) NUP85(5,4) POL32(5,9) VPS55(0,3) SSC1(1,3)
TAH11(2,3)
M10_509429_513451
Module genes
YJR035W
RAD26
Protein involved in transcription-coupled repair nucleotide
exicision repair of UV-induced DNA lesions; homolog of
human CSB protein
(153) MODULE 186
Genotype regulators
YAP1802(4,1) YGR242W FMP43(0,1) LSC2(2,3) SDA1(0,0)
BRF1(9,6) CPD1(2,6) SOL4(2,4) MGA1(3,20) YGR250C
YGR251W GCN5(0,7) PUP2(0,17) ENO1(0,4) COQ6(0,15)
GND2(2,15)
M7_985414_995892
Module genes
YGR247W
CPD1
Cyclic nucleotide phosphodiesterase, hydrolyzes ADP-ribose 1'',
2''-cyclic phosphate to ADP-ribose 1''-phosphate; no detectable
phenotype is conferred by null mutation or by overexpression
(154) MODULE 187
Genotype regulators
YGL160W YIP5(1,2) SUT1(2,13) RAD54(2,42) YRB30(1,2)
YGL165C CUP2(2,4) PMR1(4,4) HUR1(2,36) SUA5(4,8)
SPO74(4,8) ROK1(3,2) NUP49(5,0) KEM1(8,2) BUD13(2,3)
SAE2(1,3) YGL176C YGL177W MPT5(2,4) TOS3(1,10)
ATG1(0,2) GTS1(4,1)
M7_167587_192140
Module genes
YGL169W
SUA5
Protein required for respiratory growth; null mutation suppresses
the Cyc1p translation defect caused by the presence of an
aberrant ATG codon upstream of the correct start
(155) MODULE 188
Genotype regulators
ATG3(0,0) LRO1(0,0) YNR009W CSE2(3,0) PRP2(38,2)
URK1(2,1) PHO91(1,2) YNR014W SMM1(0,0) ACC1(1,2)
M14_648788_648788
Module genes
YNR013C
PHO91
Low-affinity phosphate transporter; deletion of pho84, pho87,
pho89, pho90, and pho91 causes synthetic lethality;
transcription independent of Pi and Pho4p activity;
overexpression results in vigorous growth
(156) MODULE 189
Genotype regulators
YIL002W-A CFD1(0,2) BET1(3,2) EPS1(0,0) YIL006W
NAS2(0,0) URM1(0,6) EST3(90,13) FAA3(3,6) DOT5(4,3)
TIR3(37,8) YIL012W PDR11(2,10) YIL014C-A MNT3(2,124)
YIL015C-A
M9_334195_341216
Module genes
YIL014W
MNT3
Alpha-1,3-mannosyltransferase, adds the fourth and fifth alpha1,3-linked mannose residues to O-linked glycans during protein
O-glycosylation
(157) MODULE 190
Genotype regulators
MYO1(16,4) MAS2(0,2) THR1(1,2) PPA1(0,1) RPN1(3,8)
DAP2(3,22) YHR028W-A YHR029C SLT2(0,4) RRM3(3,12)
YHR032C-A YHR032W YHR032W-A YHR033W PIH1(4,6)
YHR035W YHR036W PUT2(2,1) RRF1(2,10) MSC7(0,7)
M8_161987_176994
Module genes
YHR028C
DAP2
Dipeptidyl aminopeptidase, synthesized as a glycosylated
precursor; localizes to the vacuolar membrane; similar to Ste13p
(158) MODULE 191
Genotype regulators
M3_100213_105042
Module genes
RER1(0,0) YCL001W-A YCL001W-B YCL002C PGS1(1,1)
YCL005W VMA9(4,0) YCL006C YCL007C STP22(0,0)
ILV6(1,0) SGF29(1,0) GBP2(1,0) YCL012C YCL012W
YCL013W BUD3(10,152) DCC1(2,9) NFS1(40,7)
LEU2(246,526) YCLX10C YCLX11W YCLX12W
YCL018W
LEU2
Beta-isopropylmalate dehydrogenase, catalyzes the third step in
the leucine biosynthesis pathway
(159) MODULE 192
Genotype regulators
YLR040C YLR041W YLR042C TRX1(0,0) PDC1(0,11)
STU2(5,4) YLR046C YLR047C RPS0B(30,9) YLR049C
YLR050C YLR051C IES3(2,2) YLR053C OSW2(8,3)
SPT8(8,3) ERG3(2,12)
M12_238298_246579
Module genes
YLR050C
(160) MODULE 193
Genotype regulators
None
YAF9(3,1) YNL108C YNL109W NOP15(0,2) CYB5(0,1)
DBP2(1,2) RPC19(0,14) YNL114C YNL115C DMA2(5,1)
MLS1(2,13) DCP2(10,13) NCS2(2,2) YNL120C TOM70(1,2)
YNL122C YNL123W NAF1(5,3)
M14_402312_412269
Module genes
YNL136W
(161) MODULE 194
Genotype
regulatorsGenotype
regulators
EAF7
PRS1(0,1) FAS1(2,2) YKL183C-A LOT5(1,2) SPE1(2,1)
ASH1(1,8) MTR2(0,11) YKL187C PXA2(3,7) HYM1(1,36)
CNB1(18,1) DPH2(4,7) ACP1(1,7) SDS22(0,0) MST1(2,19)
MIA40(3,0) YKT6(0,0) PEX1(1,20) PTK1(23,2)
M11_79182_98336
Module genes
YKL187C
(162) MODULE 195
Genotype regulators
None
ARR4(0,1) DUN1(149,2) CDC2(426,139) QRI1(2,3) QRI7(4,3)
QRI2(1,2) PHO2(2,2) MSS2(4,4) KIN28(0,2) YDL109C
YDL110C RRP42(1,4) TRM3(12,5) ATG20(3,5) YDL114W
YDL114W-A IWR1(0,6)
M4_263770_273846
Module genes
YDL105W
(163) MODULE 196
Genotype regulators
QRI2
Nuclear protein of unknown function
CWC27(7,5) VPS28(2,2) YPL066W YPL067C YPL068C
BTS1(1,3) MUK1(0,0) YPL071C UBP16(2,2) YPL073C
YTA6(0,0) GCR1(5,0) GPI2(0,0) YPL077C ATP4(1,2)
RPL21B(4,0) YPL080C RPS9A(3,13) MOT1(1,4) SEN54(2,1)
BRO1(3,3) SEC16(11,3) ELP3(0,3) YDC1(0,3) YPL088W
RLM1(41,4) RPS6A(2,377)
M16_387239_420441
Module genes
YPL088W
(164) MODULE 197
Subunit of the NuA4 histone acetyltransferase complex
None
Genotype regulators
RRP12(5,1) MRPS16(0,1) YPL014W HST2(1,2) SWI1(12,30)
YPL017C CTF19(3,5) VTC3(271,210) ULP1(2,6)
ECM23(4,18) RAD1(9,2) MET12(4,2) NCE4(0,13) YPL025C
SKS1(14,5)
M16_511400_523450
Module genes
YPL016W
SWI1
(165) MODULE 198
Genotype regulators
YMR046C YMR046W-A NUP116(9,3) CSM3(3,3) ERB1(3,1)
YMR050C YMR052C-A FAR3(2,38) STB2(4,0) STV1(1,0)
BUB2(1,4) AAC1(1,15) YMR057C FET3(4,15)
M13_371857_379981
Module genes
YMR048W
CSM3
Protein required for accurate chromosome segregation during
meiosis

Supplementary materials - Stanford Artificial Intelligence Laboratory

Transcription

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