YMR175W	21.3039	MSN4	YMR175W|SIP18|S000004787|Protein of unknown function whose expression is induced by osmotic stress
YNR034W-A	20.1092	MSN4	YNR034W-A||S000007525|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p
YOL052C-A	18.1658	MSN4	YOL052C-A|DDR2|S000005413|Multistress response protein, expression is activated by a variety of xenobiotic agents and environmental or physiological stresses
YFR053C	15.0319	MSN4	YFR053C|HXK1|S000001949|Hexokinase isoenzyme 1, a cytosolic protein that catalyzes phosphorylation of glucose during glucose metabolism; expression is highest during growth on non-glucose carbon sources; glucose-induced repression involves the hexokinase Hxk2p
YKL217W	14.6912	MSN4	YKL217W|JEN1|S000001700|Lactate transporter, required for uptake of lactate and pyruvate; phosphorylated; expression is derepressed by transcriptional activator Cat8p during respiratory growth, and repressed in the presence of glucose, fructose, and mannose
YLR312C	13.3994	MSN4	YLR312C|QNQ1|S000004303|Protein of unknown function; null mutant quiescent and non-quiescent cells exhibit reduced reproductive capacity
YBR072W	12.5165	MSN4	YBR072W|HSP26|S000000276|Small heat shock protein (sHSP) with chaperone activity; forms hollow, sphere-shaped oligomers that suppress unfolded proteins aggregation; oligomer activation requires a heat-induced conformational change; not expressed in unstressed cells
YER150W	11.9592	MSN4	YER150W|SPI1|S000000952|GPI-anchored cell wall protein involved in weak acid resistance; basal expression requires Msn2p/Msn4p; expression is induced under conditions of stress and during the diauxic shift; similar to Sed1p
YMR105C	11.8273	MSN4	YMR105C|PGM2|S000004711|Phosphoglucomutase, catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism; functions as the acceptor for a Glc-phosphotransferase
YMR206W	11.8098	MSN4	YMR206W||S000004819|Putative protein of unknown function; YMR206W is not an essential gene
YOR393W	11.786	MSN4	YOR393W|ERR1|S000005920|Protein of unknown function, has similarity to enolases
YEL039C	11.474	MSN4	YEL039C|CYC7|S000000765|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
YNL117W	10.6083	MSN4	YNL117W|MLS1|S000005061|Malate synthase, enzyme of the glyoxylate cycle, involved in utilization of non-fermentable carbon sources; expression is subject to carbon catabolite repression; localizes in peroxisomes during growth in oleic acid medium
YHR096C	9.88433	MSN4	YHR096C|HXT5|S000001138|Hexose transporter with moderate affinity for glucose, induced in the presence of non-fermentable carbon sources, induced by a decrease in growth rate, contains an extended N-terminal domain relative to other HXTs
YDR343C	9.79657	MSN4	YDR343C|HXT6|S000002751|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
YOL084W	9.37707	MSN4	YOL084W|PHM7|S000005444|Protein of unknown function, expression is regulated by phosphate levels; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and vacuole
YGR087C	9.31928	MSN4	YGR087C|PDC6|S000003319|Minor isoform of pyruvate decarboxylase, decarboxylates pyruvate to acetaldehyde, involved in amino acid catabolism; transcription is glucose- and ethanol-dependent, and is strongly induced during sulfur limitation
YAR053W	8.83558	MSN4	YAR053W||S000000085|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL136W	8.46677	MSN4	YIL136W|OM45|S000001398|Protein of unknown function, major constituent of the mitochondrial outer membrane; located on the outer (cytosolic) face of the outer membrane
YMR174C	8.46643	MSN4	YMR174C|PAI3|S000004786|Cytoplasmic proteinase A (Pep4p) inhibitor, dependent on Pbs2p and Hog1p protein kinases for osmotic induction; intrinsically unstructured, N-terminal half becomes ordered in the active site of proteinase A upon contact
YOR100C	8.42777	MSN4	YOR100C|CRC1|S000005626|Mitochondrial inner membrane carnitine transporter, required for carnitine-dependent transport of acetyl-CoA from peroxisomes to mitochondria during fatty acid beta-oxidation
YFR017C	8.32271	MSN4	YFR017C||S000001913|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS; YFR017C is not an essential gene
YBR201C-A	8.32028	MSN4	YBR201C-A||S000087085|Putative protein of unknown function
YBL015W	8.04824	MSN4	YBL015W|ACH1|S000000111|Acetyl-coA hydrolase, primarily localized to mitochondria; phosphorylated; required for acetate utilization and for diploid pseudohyphal growth
YKL163W	7.71498	MSN4	YKL163W|PIR3|S000001646|O-glycosylated covalently-bound cell wall protein required for cell wall stability; expression is cell cycle regulated, peaking in M/G1 and also subject to regulation by the cell integrity pathway
YDR171W	7.66447	MSN4	YDR171W|HSP42|S000002578|Small heat shock protein (sHSP) with chaperone activity; forms barrel-shaped oligomers that suppress unfolded protein aggregation; involved in cytoskeleton reorganization after heat shock
YPL054W	7.56136	MSN4	YPL054W|LEE1|S000005975|Zinc-finger protein of unknown function
YER103W	7.47073	MSN4	YER103W|SSA4|S000000905|Heat shock protein that is highly induced upon stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the HSP70 family; cytoplasmic protein that concentrates in nuclei upon starvation
YAL061W	7.46657	MSN4	YAL061W|BDH2|S000000057|Putative medium-chain alcohol dehydrogenase with similarity to BDH1; transcription induced by constitutively active PDR1 and PDR3; BDH2 is an essential gene
YHR139C	7.30507	MSN4	YHR139C|SPS100|S000001181|Protein required for spore wall maturation; expressed during sporulation; may be a component of the spore wall
YAR060C	7.08835	MSN4	YAR060C||S000000086|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR149C	6.94142	MSN4	YLR149C||S000004139|Putative protein of unknown function; YLR149C is not an essential gene
YOR391C	6.92834	MSN4	YOR391C|HSP33|S000005918|Possible chaperone and cysteine protease with similarity to E. coli Hsp31 and S. cerevisiae Hsp31p, Hsp32p, and Sno4p; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease
YER067W	6.7872	MSN4	YER067W||S000000869|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YER067W is not an essential gene
YMR081C	6.75146	MSN4	YMR081C|ISF1|S000004686|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
YEL011W	6.74252	MSN4	YEL011W|GLC3|S000000737|Glycogen branching enzyme, involved in glycogen accumulation; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YER065C	6.63959	MSN4	YER065C|ICL1|S000000867|Isocitrate lyase, catalyzes the formation of succinate and 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
YNL194C	6.60384	MSN4	YNL194C||S000005138|Integral membrane protein localized to eisosomes; sporulation and plasma membrane sphingolipid content are altered in mutants; has homologs SUR7 and FMP45; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YHL021C	6.51808	MSN4	YHL021C|AIM17|S000001013|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YDL210W	6.51463	MSN4	YDL210W|UGA4|S000002369|Permease that serves as a gamma-aminobutyrate (GABA) transport protein involved in the utilization of GABA as a nitrogen source; catalyzes the transport of putrescine and delta-aminolevulinic acid (ALA); localized to the vacuolar membrane
YGR088W	6.39469	MSN4	YGR088W|CTT1|S000003320|Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide
YMR107W	6.29702	MSN4	YMR107W|SPG4|S000004713|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YAR050W	6.22874	MSN4	YAR050W|FLO1|S000000084|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
YBL049W	6.12469	MSN4	YBL049W|MOH1|S000000145|Protein of unknown function, has homology to kinase Snf7p; not required for growth on nonfermentable carbon sources; essential for viability in stationary phase
YDR258C	6.09744	MSN4	YDR258C|HSP78|S000002666|Oligomeric mitochondrial matrix chaperone that cooperates with Ssc1p in mitochondrial thermotolerance after heat shock; prevents the aggregation of misfolded matrix proteins; component of the mitochondrial proteolysis system
YKL026C	6.06056	MSN4	YKL026C|GPX1|S000001509|Phospholipid hydroperoxide glutathione peroxidase induced by glucose starvation that protects cells from phospholipid hydroperoxides and nonphospholipid peroxides during oxidative stress
YLR377C	6.0456	MSN4	YLR377C|FBP1|S000004369|Fructose-1,6-bisphosphatase, key regulatory enzyme in the gluconeogenesis pathway, required for glucose metabolism
YHR092C	6.00923	MSN4	YHR092C|HXT4|S000001134|High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose
YDR277C	5.95141	MSN4	YDR277C|MTH1|S000002685|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
YMR169C	5.94894	MSN4	YMR169C|ALD3|S000004779|Cytoplasmic aldehyde dehydrogenase, involved in beta-alanine synthesis; uses NAD+ as the preferred coenzyme; very similar to Ald2p; expression is induced by stress and repressed by glucose
YIL099W	5.84366	MSN4	YIL099W|SGA1|S000001361|Intracellular sporulation-specific glucoamylase involved in glycogen degradation; induced during starvation of a/a diploids late in sporulation, but dispensable for sporulation
YAL039C	5.66509	MSN4	YAL039C|CYC3|S000000037|Cytochrome c heme lyase (holocytochrome c synthase), attaches heme to apo-cytochrome c (Cyc1p or Cyc7p) in the mitochondrial intermembrane space; human ortholog may have a role in microphthalmia with linear skin defects (MLS)
YPL036W	5.64192	MSN4	YPL036W|PMA2|S000005957|Plasma membrane H+-ATPase, isoform of Pma1p, involved in pumping protons out of the cell; regulator of cytoplasmic pH and plasma membrane potential
YMR251W	5.60583	MSN4	YMR251W|GTO3|S000004863|Omega class glutathione transferase; putative cytosolic localization
YGR201C	5.60116	MSN4	YGR201C||S000003433|Putative protein of unknown function
YHR212C	5.58635	MSN4	YHR212C||S000001255|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJL089W	5.5694	MSN4	YJL089W|SIP4|S000003625|C6 zinc cluster transcriptional activator that binds to the carbon source-responsive element (CSRE) of gluconeogenic genes; involved in the positive regulation of gluconeogenesis; regulated by Snf1p protein kinase; localized to the nucleus
YPL247C	5.49447	MSN4	YPL247C||S000006168|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; similar to the petunia WD repeat protein an11; YPL247C is not an essential gene
YKL148C	5.48409	MSN4	YKL148C|SDH1|S000001631|Flavoprotein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YJR115W	5.48214	MSN4	YJR115W||S000003876|Putative protein of unknown function
YPR026W	5.43661	MSN4	YPR026W|ATH1|S000006230|Acid trehalase required for utilization of extracellular trehalose
YCR021C	5.42599	MSN4	YCR021C|HSP30|S000000615|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
YOR348C	5.339	MSN4	YOR348C|PUT4|S000005875|Proline permease, required for high-affinity transport of proline; also transports the toxic proline analog azetidine-2-carboxylate (AzC); PUT4 transcription is repressed in ammonia-grown cells
YGR243W	5.33676	MSN4	YGR243W|FMP43|S000003475|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR342C	5.19465	MSN4	YDR342C|HXT7|S000002750|High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt6p, expressed at high basal levels relative to other HXTs, expression repressed by high glucose levels
YNL093W	5.18527	MSN4	YNL093W|YPT53|S000005037|GTPase, similar to Ypt51p and Ypt52p and to mammalian rab5; required for vacuolar protein sorting and endocytosis
YBR147W	5.15669	MSN4	YBR147W|RTC2|S000000351|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays fluconazole resistance and suppresses cdc13-1 temperature sensitivity
YAL034C	5.11025	MSN4	YAL034C|FUN19|S000002134|Non-essential protein of unknown function
YAR047C	5.07561	MSN4	YAR047C||S000000083|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL230W	5.02005	MSN4	YPL230W|USV1|S000006151|Putative transcription factor containing a C2H2 zinc finger; mutation affects transcriptional regulation of genes involved in protein folding, ATP binding, and cell wall biosynthesis
YHR212W-A	4.99241	MSN4	YHR212W-A||S000028650|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YPR010C-A	4.97002	MSN4	YPR010C-A||S000122558|Putative protein of unknown function; conserved among Saccharomyces sensu stricto species
YPL271W	4.90452	MSN4	YPL271W|ATP15|S000006192|Epsilon subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YPR160W	4.78144	MSN4	YPR160W|GPH1|S000006364|Non-essential glycogen phosphorylase required for the mobilization of glycogen, activity is regulated by cyclic AMP-mediated phosphorylation, expression is regulated by stress-response elements and by the HOG MAP kinase pathway
YGR070W	4.74043	MSN4	YGR070W|ROM1|S000003302|GDP/GTP exchange protein (GEP) for Rho1p; mutations are synthetically lethal with mutations in rom2, which also encodes a GEP
YIL045W	4.67483	MSN4	YIL045W|PIG2|S000001307|Putative type-1 protein phosphatase targeting subunit that tethers Glc7p type-1 protein phosphatase to Gsy2p glycogen synthase
YHR087W	4.57003	MSN4	YHR087W|RTC3|S000001129|Protein of unknown function involved in RNA metabolism; has structural similarity to SBDS, the human protein mutated in Shwachman-Diamond Syndrome (the yeast SBDS ortholog = SDO1); null mutation suppresses cdc13-1 temperature sensitivity
YGR067C	4.54305	MSN4	YGR067C||S000003299|Putative protein of unknown function; contains a zinc finger motif similar to that of Adr1p
YDR096W	4.52715	MSN4	YDR096W|GIS1|S000002503|JmjC domain-containing histone demethylase; transcription factor involved in the expression of genes during nutrient limitation; also involved in the negative regulation of DPP1 and PHR1
YOL082W	4.52467	MSN4	YOL082W|ATG19|S000005442|Receptor protein for the cytoplasm-to-vacuole targeting (Cvt) pathway; recognizes cargo proteins aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) and delivers them to the preautophagosomal structure for packaging into Cvt vesicles
YPR184W	4.51087	MSN4	YPR184W|GDB1|S000006388|Glycogen debranching enzyme containing glucanotranferase and alpha-1,6-amyloglucosidase activities, required for glycogen degradation; phosphorylated in mitochondria
YEL008W	4.44194	MSN4	YEL008W||S000000734|Hypothetical protein predicted to be involved in metabolism
YDL204W	4.43505	MSN4	YDL204W|RTN2|S000002363|Protein of unknown function; has similarity to mammalian reticulon proteins; member of the RTNLA (reticulon-like A) subfamily
YLL026W	4.37673	MSN4	YLL026W|HSP104|S000003949|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
YPR036W-A	4.36351	MSN4	YPR036W-A||S000028425|Protein of unknown function; transcription is regulated by Pdr1p
YKL093W	4.27918	MSN4	YKL093W|MBR1|S000001576|Protein involved in mitochondrial functions and stress response; overexpression suppresses growth defects of hap2, hap3, and hap4 mutants
YJL067W	4.2577	MSN4	YJL067W||S000003603|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YFR015C	4.23302	MSN4	YFR015C|GSY1|S000001911|Glycogen synthase with similarity to Gsy2p, the more highly expressed yeast homolog; expression induced by glucose limitation, nitrogen starvation, environmental stress, and entry into stationary phase
YKL109W	4.21237	MSN4	YKL109W|HAP4|S000001592|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
YNL305C	4.20122	MSN4	YNL305C||S000005249|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YNL305C is not an essential gene
YJL103C	4.19806	MSN4	YJL103C|GSM1|S000003639|Putative zinc cluster protein of unknown function; proposed to be involved in the regulation of energy metabolism, based on patterns of expression and sequence analysis
YPL186C	4.17876	MSN4	YPL186C|UIP4|S000006107|Protein that interacts with Ulp1p, a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates; detected in a phosphorylated state in the mitochondrial outer membrane; also detected in ER and nuclear envelope
YML128C	4.17048	MSN4	YML128C|MSC1|S000004597|Protein of unknown function; mutant is defective in directing meiotic recombination events to homologous chromatids; the authentic, non-tagged protein is detected in highly purified mitochondria and is phosphorylated
YHR138C	4.17042	MSN4	YHR138C||S000001180|Putative protein of unknown function; has similarity to Pbi2p; double null mutant lacking Pbi2p and Yhr138p exhibits highly fragmented vacuoles
YBR214W	4.05863	MSN4	YBR214W|SDS24|S000000418|One of two S. cerevisiae homologs (Sds23p and Sds24p) of the Schizosaccharomyces pombe Sds23 protein, which genetic studies have implicated in APC/cyclosome regulation; may play an indirect role in fluid-phase endocytosis
YKL031W	4.01112	MSN4	YKL031W||S000001514|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species
YHL040C	4.00133	MSN4	YHL040C|ARN1|S000001032|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
YIL101C	3.9986	MSN4	YIL101C|XBP1|S000001363|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
YDL214C	3.99426	MSN4	YDL214C|PRR2|S000002373|Serine/threonine protein kinase that inhibits pheromone induced signalling downstream of MAPK, possibly at the level of the Ste12p transcription factor
YOR186W	3.94107	MSN4	YOR186W||S000005712|Putative protein of unknown function; proper regulation of expression during heat stress is sphingolipid-dependent
YFL030W	3.92368	MSN4	YFL030W|AGX1|S000001864|Alanine:glyoxylate aminotransferase (AGT), catalyzes the synthesis of glycine from glyoxylate, which is one of three pathways for glycine biosynthesis in yeast; has similarity to mammalian and plant alanine:glyoxylate aminotransferases
YDR070C	3.92239	MSN4	YDR070C|FMP16|S000002477|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR173W	3.88539	MSN4	YOR173W|DCS2|S000005699|Non-essential, stress induced regulatory protein containing a HIT (histidine triad) motif; modulates m7G-oligoribonucleotide metabolism; inhibits Dcs1p; regulated by Msn2p, Msn4p, and the Ras-cAMP-cAPK signaling pathway, similar to Dcs1p.
YEL009C	3.86772	MSN4	YEL009C|GCN4|S000000735|Transcriptional activator of amino acid biosynthetic genes in response to amino acid starvation; expression is tightly regulated at both the transcriptional and translational levels
YOR392W	3.84519	MSN4	YOR392W||S000005919|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; gene expression induced by heat
YPR027C	3.81218	MSN4	YPR027C||S000006231|Putative protein of unknown function
YAL062W	3.79118	MSN4	YAL062W|GDH3|S000000058|NADP(+)-dependent glutamate dehydrogenase, synthesizes glutamate from ammonia and alpha-ketoglutarate; rate of alpha-ketoglutarate utilization differs from Gdh1p; expression regulated by nitrogen and carbon sources
YAL054C	3.78597	MSN4	YAL054C|ACS1|S000000050|Acetyl-coA synthetase isoform which, along with Acs2p, is the nuclear source of acetyl-coA for histone acetlyation; expressed during growth on nonfermentable carbon sources and under aerobic conditions
YHR001W-A	3.77274	MSN4	YHR001W-A|QCR10|S000003529|Subunit of the ubiqunol-cytochrome c oxidoreductase complex which includes Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p and comprises part of the mitochondrial respiratory chain
YIL122W	3.75691	MSN4	YIL122W|POG1|S000001384|Putative transcriptional activator that promotes recovery from pheromone induced arrest; inhibits both alpha-factor induced G1 arrest and repression of CLN1 and CLN2 via SCB/MCB promoter elements; potential Cdc28p substrate; SBF regulated
YPL185W	3.75258	MSN4	YPL185W||S000006106|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene UIP4/YPL186C
YML100W	3.74782	MSN4	YML100W|TSL1|S000004566|Large subunit of trehalose 6-phosphate synthase (Tps1p)/phosphatase (Tps2p) complex, which converts uridine-5'-diphosphoglucose and glucose 6-phosphate to trehalose, homologous to Tps3p and may share function
YOR285W	3.72275	MSN4	YOR285W||S000005811|Protein of unknown function, localized to the mitochondrial outer membrane
YPL240C	3.69468	MSN4	YPL240C|HSP82|S000006161|Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p
YLL041C	3.68683	MSN4	YLL041C|SDH2|S000003964|Iron-sulfur protein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YGR236C	3.66083	MSN4	YGR236C|SPG1|S000003468|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR178C	3.64935	MSN4	YOR178C|GAC1|S000005704|Regulatory subunit for Glc7p type-1 protein phosphatase (PP1), tethers Glc7p to Gsy2p glycogen synthase, binds Hsf1p heat shock transcription factor, required for induction of some HSF-regulated genes under heat shock
YOL085W-A	3.57919	MSN4	YOL085W-A||S000028708|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YOL085C
YBR117C	3.56085	MSN4	YBR117C|TKL2|S000000321|Transketolase, similar to Tkl1p; catalyzes conversion of xylulose-5-phosphate and ribose-5-phosphate to sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate in the pentose phosphate pathway; needed for synthesis of aromatic amino acids
YOR120W	3.55615	MSN4	YOR120W|GCY1|S000005646|Putative NADP(+) coupled glycerol dehydrogenase, proposed to be involved in an alternative pathway for glycerol catabolism; member of the aldo-keto reductase (AKR) family
YPL223C	3.52534	MSN4	YPL223C|GRE1|S000006144|Hydrophilin of unknown function; stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway
YJL066C	3.49642	MSN4	YJL066C|MPM1|S000003602|Mitochondrial membrane protein of unknown function, contains no hydrophobic stretches
YBR269C	3.49062	MSN4	YBR269C|FMP21|S000000473|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YBL078C	3.47546	MSN4	YBL078C|ATG8|S000000174|Conserved protein that is a component of autophagosomes and Cvt vesicles; undergoes C-terminal conjugation to phosphatidylethanolamine (PE), Atg8p-PE is anchored to membranes and may mediate membrane fusion during autophagosome formation
YDL130W-A	3.47281	MSN4	YDL130W-A|STF1|S000007232|Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p may act as stabilizing factors that enhance inhibitory action of the Inh1p protein
YJR146W	3.44649	MSN4	YJR146W||S000003907|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene HMS2
YML089C	3.42946	MSN4	YML089C||S000004554|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data; expression induced by calcium shortage
YIL162W	3.42519	MSN4	YIL162W|SUC2|S000001424|Invertase, sucrose hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively
YNR001C	3.40406	MSN4	YNR001C|CIT1|S000005284|Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate; the rate-limiting enzyme of the TCA cycle; nuclear encoded mitochondrial protein
YDR119W-A	3.3966	MSN4	YDR119W-A||S000113555|Putative protein of unknown function
YJR096W	3.35068	MSN4	YJR096W||S000003857|Putative xylose and arabinose reductase; member of the aldo-keto reductase (AKR) family; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YGR258C	3.3213	MSN4	YGR258C|RAD2|S000003490|Single-stranded DNA endonuclease, cleaves single-stranded DNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPG protein
YDR234W	3.29215	MSN4	YDR234W|LYS4|S000002642|Homoaconitase, catalyzes the conversion of homocitrate to homoisocitrate, which is a step in the lysine biosynthesis pathway
YIL066C	3.28438	MSN4	YIL066C|RNR3|S000001328|One of two large regulatory subunits of ribonucleotide-diphosphate reductase; the RNR complex catalyzes rate-limiting step in dNTP synthesis, regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits
YGR248W	3.25214	MSN4	YGR248W|SOL4|S000003480|6-phosphogluconolactonase with similarity to Sol3p
YDL169C	3.23191	MSN4	YDL169C|UGX2|S000002328|Protein of unknown function, transcript accumulates in response to any combination of stress conditions
YDL181W	3.22824	MSN4	YDL181W|INH1|S000002340|Protein that inhibits ATP hydrolysis by the F1F0-ATP synthase; inhibitory function is enhanced by stabilizing proteins Stf1p and Stf2p; has similarity to Stf1p; has a calmodulin-binding motif and binds calmodulin in vitro
YLR258W	3.22001	MSN4	YLR258W|GSY2|S000004248|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
YMR250W	3.20473	MSN4	YMR250W|GAD1|S000004862|Glutamate decarboxylase, converts glutamate into gamma-aminobutyric acid (GABA) during glutamate catabolism; involved in response to oxidative stress
YPL017C	3.19586	MSN4	YPL017C|IRC15|S000005938|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family, required for accurate meiotic chromosome segregation; null mutant displays increased levels of spontaneous Rad52 foci
YIL057C	3.18648	MSN4	YIL057C||S000001319|Putative protein of unknown function; expression induced under carbon limitation and repressed under high glucose
YJL144W	3.17806	MSN4	YJL144W||S000003680|Cytoplasmic hydrophilin of unknown function, possibly involved in the dessication response; expression induced by osmotic stress, starvation and during stationary phase; GFP-fusion protein is induced by the DNA-damaging agent MMS
YKL085W	3.17527	MSN4	YKL085W|MDH1|S000001568|Mitochondrial malate dehydrogenase, catalyzes interconversion of malate and oxaloacetate; involved in the tricarboxylic acid (TCA) cycle; phosphorylated
YIR039C	3.13831	MSN4	YIR039C|YPS6|S000001478|Putative GPI-anchored aspartic protease
YMR118C	3.11834	MSN4	YMR118C||S000004724|Protein of unknown function with similarity to succinate dehydrogenase cytochrome b subunit; YMR118C is not an essential gene
YML120C	3.11335	MSN4	YML120C|NDI1|S000004589|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; phosphorylated; homolog of human AMID
YOR066W	3.09263	MSN4	YOR066W|MSA1|S000005592|Activator of G1-specific transcription factors, MBF and SBF, that regulates both the timing of G1-specific gene transcription, and cell cycle initiation; potential Cdc28p substrate
YPL250C	3.08903	MSN4	YPL250C|ICY2|S000006171|Protein of unknown function; mobilized into polysomes upon a shift from a fermentable to nonfermentable carbon source; potential Cdc28p substrate
YMR194C-B	3.08364	MSN4	YMR194C-B||S000028514|Putative protein of unknown function
YAL005C	3.07287	MSN4	YAL005C|SSA1|S000000004|ATPase involved in protein folding and nuclear localization signal (NLS)-directed nuclear transport; member of heat shock protein 70 (HSP70) family; forms a chaperone complex with Ydj1p; localized to the nucleus, cytoplasm, and cell wall
YLR080W	3.06029	MSN4	YLR080W|EMP46|S000004070|Integral membrane component of endoplasmic reticulum-derived COPII-coated vesicles, which function in ER to Golgi transport
YMR181C	3.05604	MSN4	YMR181C||S000004793|Protein of unknown function; mRNA transcribed as part of a bicistronic transcript with a predicted transcriptional repressor RGM1/YMR182C; mRNA is destroyed by nonsense-mediated decay (NMD); YMR181C is not an essential gene
YJL141C	3.04072	MSN4	YJL141C|YAK1|S000003677|Serine-threonine protein kinase that is part of a glucose-sensing system involved in growth control in response to glucose availability; translocates from the cytoplasm to the nucleus and phosphorylates Pop2p in response to a glucose signal
YFL058W	3.03204	MSN4	YFL058W|THI5|S000001836|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YOL118C	3.03115	MSN4	YOL118C||S000005478|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YGL045W	3.01668	MSN4	YGL045W|RIM8|S000003013|Protein of unknown function, involved in the proteolytic activation of Rim101p in response to alkaline pH; has similarity to A. nidulans PalF
YJL045W	2.98579	MSN4	YJL045W||S000003581|Minor succinate dehydrogenase isozyme; homologous to Sdh1p, the major isozyme reponsible for the oxidation of succinate and transfer of electrons to ubiquinone; induced during the diauxic shift in a Cat8p-dependent manner
YOL060C	2.982	MSN4	YOL060C|MAM3|S000005421|Protein required for normal mitochondrial morphology, has similarity to hemolysins
YJL116C	2.95742	MSN4	YJL116C|NCA3|S000003652|Protein that functions with Nca2p to regulate mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p ) of the Fo-F1 ATP synthase; member of the SUN family
YNL077W	2.94634	MSN4	YNL077W|APJ1|S000005021|Putative chaperone of the HSP40 (DNAJ) family; overexpression interferes with propagation of the [Psi+] prion; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YMR017W	2.92893	MSN4	YMR017W|SPO20|S000004619|Meiosis-specific subunit of the t-SNARE complex, required for prospore membrane formation during sporulation; similar to but not functionally redundant with Sec9p; SNAP-25 homolog
YLL053C	2.88233	MSN4	YLL053C||S000003976|Putative protein; in the Sigma 1278B strain background YLL053C is contiguous with AQY2 which encodes an aquaporin
YLR294C	2.86254	MSN4	YLR294C||S000004285|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene ATP14
YMR244W	2.85277	MSN4	YMR244W||S000004858|Putative protein of unknown function
YLR122C	2.84711	MSN4	YLR122C||S000004112|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR123C
YOR346W	2.82938	MSN4	YOR346W|REV1|S000005873|Deoxycytidyl transferase, forms a complex with the subunits of DNA polymerase zeta, Rev3p and Rev7p; involved in repair of abasic sites in damaged DNA
YLL019C	2.81231	MSN4	YLL019C|KNS1|S000003942|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
YDR018C	2.81143	MSN4	YDR018C||S000002425|Probable membrane protein with three predicted transmembrane domains; homologous to Ybr042cp, similar to C. elegans F55A11.5 and maize 1-acyl-glycerol-3-phosphate acyltransferase; null exhibits no apparent phenotype
YIL100C-A	2.80207	MSN4	YIL100C-A||S000028794|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOL154W	2.79922	MSN4	YOL154W|ZPS1|S000005514|Putative GPI-anchored protein; transcription is induced under low-zinc conditions, as mediated by the Zap1p transcription factor, and at alkaline pH
YBR050C	2.76845	MSN4	YBR050C|REG2|S000000254|Regulatory subunit of the Glc7p type-1 protein phosphatase; involved with Reg1p, Glc7p, and Snf1p in regulation of glucose-repressible genes, also involved in glucose-induced proteolysis of maltose permease
YDR178W	2.75848	MSN4	YDR178W|SDH4|S000002585|Membrane anchor subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YLR178C	2.74788	MSN4	YLR178C|TFS1|S000004168|Carboxypeptidase Y inhibitor, function requires acetylation by the NatB N-terminal acetyltransferase; phosphatidylethanolamine-binding protein involved in protein kinase A signaling pathway
YOR374W	2.74348	MSN4	YOR374W|ALD4|S000005901|Mitochondrial aldehyde dehydrogenase, required for growth on ethanol and conversion of acetaldehyde to acetate; phosphorylated; activity is K+ dependent; utilizes NADP+ or NAD+ equally as coenzymes; expression is glucose repressed
YBR051W	2.74209	MSN4	YBR051W||S000000255|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partiallly overlaps the REG2/YBR050C regulatory subunit of the Glc7p type-1 protein phosphatase
YBR183W	2.73983	MSN4	YBR183W|YPC1|S000000387|Alkaline ceramidase that also has reverse (CoA-independent) ceramide synthase activity, catalyzes both breakdown and synthesis of phytoceramide; overexpression confers fumonisin B1 resistance
YOR211C	2.73339	MSN4	YOR211C|MGM1|S000005737|Mitochondrial GTPase related to dynamin, present in a complex containing Ugo1p and Fzo1p; required for normal morphology of cristae and for stability of Tim11p; homolog of human OPA1 involved in autosomal dominant optic atrophy
YFR022W	2.7312	MSN4	YFR022W|ROG3|S000001918|Protein that binds to Rsp5p, which is a hect-type ubiquitin ligase, via its 2 PY motifs; has similarity to Rod1p; mutation suppresses the temperature sensitivity of an mck1 rim11 double mutant
YGR069W	2.71434	MSN4	YGR069W||S000003301|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR230C	2.70221	MSN4	YBR230C|OM14|S000000434|Integral mitochondrial outer membrane protein; abundance is decreased in cells grown in glucose relative to other carbon sources; appears to contain 3 alpha-helical transmembrane segments; ORF encodes a 97-basepair intron
YFL052W	2.6752	MSN4	YFL052W||S000001842|Putative zinc cluster protein that contains a DNA binding domain; null mutant sensitive to calcofluor white, low osmolarity and heat, suggesting a role for YFL052Wp in cell wall integrity
YOL047C	2.66962	MSN4	YOL047C||S000005407|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YEL070W	2.65402	MSN4	YEL070W|DSF1|S000000796|Deletion suppressor of mpt5 mutation
YGR256W	2.64927	MSN4	YGR256W|GND2|S000003488|6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone
YOR065W	2.63655	MSN4	YOR065W|CYT1|S000005591|Cytochrome c1, component of the mitochondrial respiratory chain; expression is regulated by the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex
YOR382W	2.62423	MSN4	YOR382W|FIT2|S000005909|Mannoprotein that is incorporated into the cell wall via a glycosylphosphatidylinositol (GPI) anchor, involved in the retention of siderophore-iron in the cell wall
YKL107W	2.61424	MSN4	YKL107W||S000001590|Putative protein of unknown function
YPL156C	2.60704	MSN4	YPL156C|PRM4|S000006077|Pheromone-regulated protein, predicted to have 1 transmembrane segment; transcriptionally regulated by Ste12p during mating and by Cat8p during the diauxic shift
YPL229W	2.60224	MSN4	YPL229W||S000006150|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL229W is not an essential gene
YKL177W	2.60041	MSN4	YKL177W||S000001660|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene STE3
YFL054C	2.59548	MSN4	YFL054C||S000001840|Putative channel-like protein; similar to Fps1p; mediates passive diffusion of glycerol in the presence of ethanol
YMR280C	2.58761	MSN4	YMR280C|CAT8|S000004893|Zinc cluster transcriptional activator necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements
YER088C	2.58426	MSN4	YER088C|DOT6|S000000890|Protein of unknown function, involved in telomeric gene silencing and filamentation
YMR297W	2.58133	MSN4	YMR297W|PRC1|S000004912|Vacuolar carboxypeptidase Y (proteinase C), broad-specificity C-terminal exopeptidase involved in non-specific protein degradation in the vacuole; member of the serine carboxypeptidase family
YBR132C	2.57947	MSN4	YBR132C|AGP2|S000000336|High affinity polyamine permease, preferentially uses spermidine over putrescine; expression is down-regulated by osmotic stress; plasma membrane carnitine transporter, also functions as a low-affinity amino acid permease
YLL052C	2.53454	MSN4	YLL052C|AQY2|S000003975|Water channel that mediates the transport of water across cell membranes, only expressed in proliferating cells, controlled by osmotic signals, may be involved in freeze tolerance; disrupted by a stop codon in many S. cerevisiae strains
YCR005C	2.52416	MSN4	YCR005C|CIT2|S000000598|Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate, peroxisomal isozyme involved in glyoxylate cycle; expression is controlled by Rtg1p and Rtg2p transcription factors
YJL102W	2.51601	MSN4	YJL102W|MEF2|S000003638|Mitochondrial elongation factor involved in translational elongation
YMR196W	2.50762	MSN4	YMR196W||S000004809|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR196W is not an essential gene
YNL055C	2.50372	MSN4	YNL055C|POR1|S000005000|Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated
YGL096W	2.50169	MSN4	YGL096W|TOS8|S000003064|Homeodomain-containing transcription factor; SBF regulated target gene that in turn regulates expression of genes involved in G1/S phase events such as bud site selection, bud emergence and cell cycle progression; similarity to Cup9p
YIL113W	2.49908	MSN4	YIL113W|SDP1|S000001375|Stress-inducible dual-specificity MAP kinase phosphatase, negatively regulates Slt2p MAP kinase by direct dephosphorylation, diffuse localization under normal conditions shifts to punctate localization after heat shock
YKR067W	2.47491	MSN4	YKR067W|GPT2|S000001775|Glycerol-3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase located in lipid particles and the ER; involved in the stepwise acylation of glycerol-3-phosphate and dihydroxyacetone in lipid biosynthesis
YER039C-A	2.46272	MSN4	YER039C-A||S000007226|Putative protein of unknown function; YER039C-A is not an essential gene
YNL190W	2.45447	MSN4	YNL190W||S000005134|Cell wall protein of unknown function; proposed role as a hydrophilin induced by osmotic stress; contains a putative GPI-attachment site
YNL180C	2.44635	MSN4	YNL180C|RHO5|S000005124|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
YKL067W	2.43434	MSN4	YKL067W|YNK1|S000001550|Nucleoside diphosphate kinase, catalyzes the transfer of gamma phosphates from nucleoside triphosphates, usually ATP, to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate
YGL184C	2.40423	MSN4	YGL184C|STR3|S000003152|Cystathionine beta-lyase, converts cystathionine into homocysteine
YKR066C	2.40197	MSN4	YKR066C|CCP1|S000001774|Mitochondrial cytochrome-c peroxidase; degrades reactive oxygen species in mitochondria, involved in the response to oxidative stress
YER066W	2.39693	MSN4	YER066W||S000000868|Putative protein of unknown function; YER066W is not an essential gene
YGL104C	2.39139	MSN4	YGL104C|VPS73|S000003072|Mitochondrial protein; mutation affects vacuolar protein sorting; putative transporter; member of the sugar porter family
YDR516C	2.38577	MSN4	YDR516C|EMI2|S000002924|Non-essential protein of unknown function required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulation; expression is regulated by glucose-repression transcription factors Mig1/2p
YGR144W	2.38377	MSN4	YGR144W|THI4|S000003376|Thiazole synthase, catalyzes formation of the thiazole moiety of thiamin pyrophosphate; required for thiamine biosynthesis and for mitochondrial genome stability
YNL322C	2.36117	MSN4	YNL322C|KRE1|S000005266|Cell wall glycoprotein involved in beta-glucan assembly; serves as a K1 killer toxin membrane receptor
YOR345C	2.35175	MSN4	YOR345C||S000005872|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene REV1; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YOL119C	2.3508	MSN4	YOL119C|MCH4|S000005479|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
YDL004W	2.33384	MSN4	YDL004W|ATP16|S000002162|Delta subunit of the central stalk of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YKL146W	2.33373	MSN4	YKL146W|AVT3|S000001629|Vacuolar transporter, exports large neutral amino acids from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YOR343C	2.32057	MSN4	YOR343C||S000005870|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YLR123C	2.31032	MSN4	YLR123C||S000004113|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR122C; contains characteristic aminoacyl-tRNA motif
YPL092W	2.30041	MSN4	YPL092W|SSU1|S000006013|Plasma membrane sulfite pump involved in sulfite metabolism and required for efficient sulfite efflux; major facilitator superfamily protein
YMR090W	2.28231	MSN4	YMR090W||S000004696|Putative protein of unknown function with similarity to DTDP-glucose 4,6-dehydratases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR090W is not an essential gene
YCR010C	2.27335	MSN4	YCR010C|ADY2|S000000603|Acetate transporter required for normal sporulation; phosphorylated in mitochondria
YFL019C	2.2649	MSN4	YFL019C||S000001875|Dubious open reading frame unlikely to encode a protein; YFL019C is not an essential gene
YPR007C	2.25348	MSN4	YPR007C|REC8|S000006211|Meiosis-specific component of sister chromatid cohesion complex; maintains cohesion between sister chromatids during meiosis I; maintains cohesion between centromeres of sister chromatids until meiosis II; homolog of S. pombe Rec8p
YPL006W	2.25069	MSN4	YPL006W|NCR1|S000005927|Vacuolar membrane protein that transits through the biosynthetic vacuolar protein sorting pathway, involved in sphingolipid metabolism; glycoprotein and functional orthologue of human Niemann Pick C1 (NPC1) protein
YPL119C	2.24364	MSN4	YPL119C|DBP1|S000006040|Putative ATP-dependent RNA helicase of the DEAD-box protein family; mutants show reduced stability of the 40S ribosomal subunit scanning through 5' untranslated regions of mRNAs
YLR152C	2.2277	MSN4	YLR152C||S000004142|Putative protein of unknown function; YLR152C is not an essential gene
YLR346C	2.21431	MSN4	YLR346C||S000004338|Putative protein of unknown function found in mitochondria; expression is regulated by transcription factors involved in pleiotropic drug resistance, Pdr1p and Yrr1p; YLR346C is not an essential gene
YKL147C	2.19559	MSN4	YKL147C||S000001630|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene AVT3
YNL179C	2.19419	MSN4	YNL179C||S000005123|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; deletion in cyr1 mutant results in loss of stress resistance
YDR001C	2.18131	MSN4	YDR001C|NTH1|S000002408|Neutral trehalase, degrades trehalose; required for thermotolerance and may mediate resistance to other cellular stresses; may be phosphorylated by Cdc28p
YBR280C	2.17326	MSN4	YBR280C|SAF1|S000000484|F-Box protein involved in proteasome-dependent degradation of Aah1p during entry of cells into quiescence; interacts with Skp1
YIL100W	2.16856	MSN4	YIL100W||S000001362|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the dubious ORF YIL100C-A
YNL014W	2.16527	MSN4	YNL014W|HEF3|S000004959|Translational elongation factor EF-3; paralog of YEF3 and member of the ABC superfamily; stimulates EF-1 alpha-dependent binding of aminoacyl-tRNA by the ribosome; normally expressed in zinc deficient cells
YPR196W	2.1549	MSN4	YPR196W||S000006400|Putative maltose activator
YOR376W	2.15341	MSN4	YOR376W||S000005903|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YOR376W is not an essential gene.
YBR203W	2.15217	MSN4	YBR203W|COS111|S000000407|Protein required for resistance to the antifungal drug ciclopirox olamine; not related to the subtelomerically-encoded COS family; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YML118W	2.14157	MSN4	YML118W|NGL3|S000004587|Putative endonuclease, has a domain similar to a magnesium-dependent endonuclease motif in mRNA deadenylase Ccr4p; similar to Ngl1p and Ngl2p
YIR027C	2.13475	MSN4	YIR027C|DAL1|S000001466|Allantoinase, converts allantoin to allantoate in the first step of allantoin degradation; expression sensitive to nitrogen catabolite repression
YBR241C	2.12735	MSN4	YBR241C||S000000445|Putative transporter, member of the sugar porter family; green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane; YBR241C is not an essential gene
YLR296W	2.1233	MSN4	YLR296W||S000004287|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLL055W	2.11521	MSN4	YLL055W|YCT1|S000003978|High-affinity cysteine-specific transporter with similarity to the Dal5p family of transporters; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YCT1 is not an essential gene
YDL113C	2.10934	MSN4	YDL113C|ATG20|S000002271|Sorting nexin family member required for the cytoplasm-to-vacuole targeting (Cvt) pathway and for endosomal sorting; has a Phox homology domain that binds phosphatidylinositol-3-phosphate; interacts with Snx4p; potential Cdc28p substrate
YBR298C	2.10924	MSN4	YBR298C|MAL31|S000000502|Maltose permease, high-affinity maltose transporter (alpha-glucoside transporter); encoded in the MAL3 complex locus; member of the 12 transmembrane domain superfamily of sugar transporters; functional in genomic reference strain S288C
YGR043C	2.10883	MSN4	YGR043C|NQM1|S000003275|Protein of unknown function; transcription is repressed by Mot1p and induced by alpha-factor and during diauxic shift; null mutant non-quiescent cells exhibit reduced reproductive capacity
YKL010C	2.10679	MSN4	YKL010C|UFD4|S000001493|Ubiquitin-protein ligase (E3) that interacts with Rpt4p and Rpt6p, two subunits of the 19S particle of the 26S proteasome; cytoplasmic E3 involved in the degradation of ubiquitin fusion proteins
YHR104W	2.09741	MSN4	YHR104W|GRE3|S000001146|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
YKL044W	2.08796	MSN4	YKL044W||S000001527|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR326W	2.08538	MSN4	YLR326W||S000004318|Hypothetical protein
YER084W	2.0837	MSN4	YER084W||S000000886|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR247W	2.06791	MSN4	YDR247W|VHS1|S000002655|Cytoplasmic serine/threonine protein kinase; identified as a high-copy suppressor of the synthetic lethality of a sis2 sit4 double mutant, suggesting a role in G1/S phase progression; homolog of Sks1p
YBL064C	2.06118	MSN4	YBL064C|PRX1|S000000160|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; phosphorylated
YJR149W	2.06025	MSN4	YJR149W||S000003910|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YJR091C	2.05617	MSN4	YJR091C|JSN1|S000003851|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
YHL036W	2.0465	MSN4	YHL036W|MUP3|S000001028|Low affinity methionine permease, similar to Mup1p
YKL103C	2.04464	MSN4	YKL103C|LAP4|S000001586|Vacuolar aminopeptidase, often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathway
YJR008W	2.04425	MSN4	YJR008W||S000003768|Putative protein of unknown function; expression repressed by inosine and choline in an Opi1p-dependent manner; expression induced by mild heat-stress on a non-fermentable carbon source.
YHL024W	2.03831	MSN4	YHL024W|RIM4|S000001016|Putative RNA-binding protein required for the expression of early and middle sporulation genes
YEL009C-A	2.03123	MSN4	YEL009C-A||S000028741|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YAL060W	2.03098	MSN4	YAL060W|BDH1|S000000056|NAD-dependent (R,R)-butanediol dehydrogenase, catalyzes oxidation of (R,R)-2,3-butanediol to (3R)-acetoin, oxidation of meso-butanediol to (3S)-acetoin, and reduction of acetoin; enhances use of 2,3-butanediol as an aerobic carbon source
YDL079C	2.0222	MSN4	YDL079C|MRK1|S000002237|Glycogen synthase kinase 3 (GSK-3) homolog; one of four GSK-3 homologs in S. cerevisiae that function to activate Msn2p-dependent transcription of stress responsive genes and that function in protein degradation
YJR085C	2.02125	MSN4	YJR085C||S000003845|Putative protein of unknown function; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR327C	2.01565	MSN4	YLR327C|TMA10|S000004319|Protein of unknown function that associates with ribosomes
YBR139W	2.00338	MSN4	YBR139W||S000000343|Putative serine type carboxypeptidase with a role in phytochelatin synthesis; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner
YOR298C-A	2.00205	MSN4	YOR298C-A|MBF1|S000007253|Transcriptional coactivator that bridges the DNA-binding region of Gcn4p and TATA-binding protein Spt15p; suppressor of frameshift mutations
YCL048W-A	1.99642	MSN4	YCL048W-A||S000087203|Putative protein of unknown function
YGR194C	1.97876	MSN4	YGR194C|XKS1|S000003426|Xylulokinase, converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains
YJL005W	1.97663	MSN4	YJL005W|CYR1|S000003542|Adenylate cyclase, required for cAMP production and cAMP-dependent protein kinase signaling; the cAMP pathway controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation
YKL178C	1.96732	MSN4	YKL178C|STE3|S000001661|Receptor for a factor receptor, transcribed in alpha cells and required for mating by alpha cells, couples to MAP kinase cascade to mediate pheromone response; ligand bound receptors are endocytosed and recycled to the plasma membrane; GPCR
YML090W	1.96684	MSN4	YML090W||S000004555|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YML089C; exhibits growth defect on a non-fermentable (respiratory) carbon source
YEL059W	1.96433	MSN4	YEL059W||S000000785|Dubious open reading frame unlikely to encode a functional protein
YCL025C	1.96375	MSN4	YCL025C|AGP1|S000000530|Low-affinity amino acid permease with broad substrate range, involved in uptake of asparagine, glutamine, and other amino acids; expression is regulated by the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p)
YIL059C	1.96253	MSN4	YIL059C||S000001321|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YIL060W
YGL072C	1.95931	MSN4	YGL072C||S000003040|Dubious open reading frame unlikely to encode a protein; partially overlaps the verified gene HSF1; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YKR049C	1.9548	MSN4	YKR049C|FMP46|S000001757|Putative redox protein containing a thioredoxin fold; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YMR135C	1.95049	MSN4	YMR135C|GID8|S000004742|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains LisH and CTLH domains, like Vid30p; dosage-dependent regulator of START
YLR295C	1.94572	MSN4	YLR295C|ATP14|S000004286|Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YOR152C	1.94499	MSN4	YOR152C||S000005678|Putative protein of unknown function; has no similarity to any known protein; YOR152C is not an essential gene
YMR103C	1.92949	MSN4	YMR103C||S000004709|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR030W	1.92796	MSN4	YLR030W||S000004020|Putative protein of unknown function
YOR031W	1.91315	MSN4	YOR031W|CRS5|S000005557|Copper-binding metallothionein, required for wild-type copper resistance
YLL056C	1.90551	MSN4	YLL056C||S000003979|Putative protein of unknown function, transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in pleiotropic drug resistance (PDR) phenomenon; YLL056C is not an essential gene
YOL163W	1.89343	MSN4	YOL163W||S000005523|Putative protein of unknown function; member of the Dal5p subfamily of the major facilitator family
YDL196W	1.88879	MSN4	YDL196W||S000002355|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; open reading frame is located in promoter region of essential gene SEC31
YIL125W	1.8775	MSN4	YIL125W|KGD1|S000001387|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
YFL011W	1.87733	MSN4	YFL011W|HXT10|S000001883|Putative hexose transporter, expressed at low levels and expression is repressed by glucose
YER096W	1.86893	MSN4	YER096W|SHC1|S000000898|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
YER101C	1.86556	MSN4	YER101C|AST2|S000000903|Protein that may have a role in targeting of plasma membrane [H+]ATPase (Pma1p) to the plasma membrane, as suggested by analysis of genetic interactions
YOR049C	1.86156	MSN4	YOR049C|RSB1|S000005575|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
YDR250C	1.86066	MSN4	YDR250C||S000002658|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YIL146C	1.8584	MSN4	YIL146C|ECM37|S000001408|Non-essential protein of unknown function
YIL055C	1.8487	MSN4	YIL055C||S000001317|Putative protein of unknown function
YDR529C	1.82997	MSN4	YDR529C|QCR7|S000002937|Subunit 7 of the ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; oriented facing the mitochondrial matrix; N-terminus appears to play a role in complex assembly
YER054C	1.81925	MSN4	YER054C|GIP2|S000000856|Putative regulatory subunit of the protein phosphatase Glc7p, involved in glycogen metabolism; contains a conserved motif (GVNK motif) that is also found in Gac1p, Pig1p, and Pig2p
YIL155C	1.81691	MSN4	YIL155C|GUT2|S000001417|Mitochondrial glycerol-3-phosphate dehydrogenase; expression is repressed by both glucose and cAMP and derepressed by non-fermentable carbon sources in a Snf1p, Rsf1p, Hap2/3/4/5 complex dependent manner
YDR043C	1.80958	MSN4	YDR043C|NRG1|S000002450|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
YJR120W	1.79565	MSN4	YJR120W||S000003881|Protein of unknown function; essential for growth under anaerobic conditions; mutation causes decreased expression of ATP2, impaired respiration, defective sterol uptake, and altered levels/localization of ABC transporters Aus1p and Pdr11p
YHR139C-A	1.7955	MSN4	YHR139C-A||S000003533|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCL035C	1.79537	MSN4	YCL035C|GRX1|S000000540|Hydroperoxide and superoxide-radical responsive heat-stable glutathione-dependent disulfide oxidoreductase with active site cysteine pair; protects cells from oxidative damage
YPL087W	1.79439	MSN4	YPL087W|YDC1|S000006008|Alkaline dihydroceramidase, involved in sphingolipid metabolism; preferentially hydrolyzes dihydroceramide to a free fatty acid and dihydrosphingosine; has a minor reverse activity
YHR199C	1.79132	MSN4	YHR199C|AIM46|S000001242|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YHR008C	1.78817	MSN4	YHR008C|SOD2|S000001050|Mitochondrial superoxide dismutase, protects cells against oxygen toxicity; phosphorylated
YCR030C	1.78791	MSN4	YCR030C|SYP1|S000000626|Protein with a potential role in actin cytoskeletal organization; overexpression suppresses a pfy1 (profilin) null mutation
YJL155C	1.7871	MSN4	YJL155C|FBP26|S000003691|Fructose-2,6-bisphosphatase, required for glucose metabolism
YEL049W	1.77959	MSN4	YEL049W|PAU2|S000000775|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
YPR013C	1.76904	MSN4	YPR013C||S000006217|Putative zinc finger protein; YPR013C is not an essential gene
YLR332W	1.76833	MSN4	YLR332W|MID2|S000004324|O-glycosylated plasma membrane protein that acts as a sensor for cell wall integrity signaling and activates the pathway; interacts with Rom2p, a guanine nucleotide exchange factor for Rho1p, and with cell integrity pathway protein Zeo1p
YCR011C	1.76668	MSN4	YCR011C|ADP1|S000000604|Putative ATP-dependent permease of the ABC transporter family of proteins
YNL332W	1.75949	MSN4	YNL332W|THI12|S000005276|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YNL144C	1.74497	MSN4	YNL144C||S000005088|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YNL144C is not an essential gene
YOL110W	1.74148	MSN4	YOL110W|SHR5|S000005470|Subunit of a palmitoyltransferase, composed of Shr5p and Erf2p, that adds a palmitoyl lipid moiety to heterolipidated substrates such as Ras1p and Ras2p through a thioester linkage; palmitoylation is required for Ras2p membrane localization
YDR262W	1.74048	MSN4	YDR262W||S000002670|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole and is induced in response to the DNA-damaging agent MMS; gene expression increases in response to Zymoliase treatment
YPR028W	1.73917	MSN4	YPR028W|YOP1|S000006232|Membrane protein that interacts with Yip1p to mediate membrane traffic; overexpression results in cell death and accumulation of internal cell membranes; regulates vesicular traffic in stressed cells
YER121W	1.72848	MSN4	YER121W||S000000923|Putative protein of unknown function; may be involved in phosphatase regulation and/or generation of precursor metabolites and energy
YLR331C	1.72504	MSN4	YLR331C|JIP3|S000004323|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 98% of ORF overlaps the verified gene MID2
YDR251W	1.72227	MSN4	YDR251W|PAM1|S000002659|Essential protein of unknown function; exhibits variable expression during colony morphogenesis; overexpression permits survival without protein phosphatase 2A, inhibits growth, and induces a filamentous phenotype
YIL086C	1.71316	MSN4	YIL086C||S000001348|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR379C-A	1.71213	MSN4	YDR379C-A||S000007605|Hypothetical protein identified by homology. See FEBS Letters [2000] 487:31-36.
YDR259C	1.7086	MSN4	YDR259C|YAP6|S000002667|Putative basic leucine zipper (bZIP) transcription factor; overexpression increases sodium and lithium tolerance
YDL021W	1.69737	MSN4	YDL021W|GPM2|S000002179|Homolog of Gpm1p phosphoglycerate mutase which converts 3-phosphoglycerate to 2-phosphoglycerate in glycolysis; may be non-functional derivative of a gene duplication event
YDR148C	1.69163	MSN4	YDR148C|KGD2|S000002555|Dihydrolipoyl transsuccinylase, component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes the oxidative decarboxylation of alpha-ketoglutarate to succinyl-CoA in the TCA cycle; phosphorylated
YDR403W	1.69129	MSN4	YDR403W|DIT1|S000002811|Sporulation-specific enzyme required for spore wall maturation, involved in the production of a soluble LL-dityrosine-containing precursor of the spore wall; transcripts accumulate at the time of prospore enclosure
YIL087C	1.6907	MSN4	YIL087C|LRC2|S000001349|Putative protein of unknown function; protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased mitochondrial genome loss (petite formation) and severe growth defect in minimal glycerol media
YHR097C	1.68483	MSN4	YHR097C||S000001139|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus
YIL107C	1.67389	MSN4	YIL107C|PFK26|S000001369|6-phosphofructo-2-kinase, inhibited by phosphoenolpyruvate and sn-glycerol 3-phosphate, has negligible fructose-2,6-bisphosphatase activity, transcriptional regulation involves protein kinase A
YDR249C	1.67299	MSN4	YDR249C||S000002657|Putative protein of unknown function
YNL074C	1.66887	MSN4	YNL074C|MLF3|S000005018|Serine-rich protein of unknown function; overproduction suppresses the growth inhibition caused by exposure to the immunosuppressant leflunomide
YJL037W	1.66775	MSN4	YJL037W|IRC18|S000003574|Putative protein of unknown function; expression induced in respiratory-deficient cells and in carbon-limited chemostat cultures; similar to adjacent ORF, YJL038C; null mutant displays increased levels of spontaneous Rad52p foci
YJL161W	1.65713	MSN4	YJL161W|FMP33|S000003697|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR032C	1.65669	MSN4	YDR032C|PST2|S000002439|Protein with similarity to members of a family of flavodoxin-like proteins; induced by oxidative stress in a Yap1p dependent manner; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGR023W	1.63576	MSN4	YGR023W|MTL1|S000003255|Protein with both structural and functional similarity to Mid2p, which is a plasma membrane sensor required for cell integrity signaling during pheromone-induced morphogenesis; suppresses rgd1 null mutations
YJL213W	1.62511	MSN4	YJL213W||S000003749|Protein of unknown function that may interact with ribosomes; periodically expressed during the yeast metabolic cycle; phosphorylated in vitro by the mitotic exit network (MEN) kinase complex, Dbf2p/Mob1p
YGL258W-A	1.62289	MSN4	YGL258W-A||S000007607|Putative protein of unknown function
YAL028W	1.60501	MSN4	YAL028W|FRT2|S000000026|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
YMR195W	1.59511	MSN4	YMR195W|ICY1|S000004808|Protein of unknown function, required for viability in rich media of cells lacking mitochondrial DNA; mutants have an invasive growth defect with elongated morphology; induced by amino acid starvation
YDR223W	1.58771	MSN4	YDR223W|CRF1|S000002631|Transcriptional corepressor involved in the regulation of ribosomal protein gene transcription via the TOR signaling pathway and protein kinase A, phosphorylated by activated Yak1p which promotes accumulation of Crf1p in the nucleus
YBR212W	1.5807	MSN4	YBR212W|NGR1|S000000416|RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochondrial porin (POR1) mRNA and enhances its degradation; overexpression impairs mitochondrial function; expressed in stationary phase
YDL085W	1.58042	MSN4	YDL085W|NDE2|S000002243|Mitochondrial external NADH dehydrogenase, catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p are involved in providing the cytosolic NADH to the mitochondrial respiratory chain
YPL272C	1.57977	MSN4	YPL272C||S000006193|Putative protein of unknown function; gene expression induced in response to ketoconazole; YPL272C is not an essential gene
YKR034W	1.56593	MSN4	YKR034W|DAL80|S000001742|Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with Deh1p
YER035W	1.56226	MSN4	YER035W|EDC2|S000000837|RNA-binding protein, activates mRNA decapping directly by binding to the mRNA substrate and enhancing the activity of the decapping proteins Dcp1p and Dcp2p
YIL017C	1.55588	MSN4	YIL017C|VID28|S000001279|Protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); localized to the nucleus and the cytoplasm
YJL151C	1.55238	MSN4	YJL151C|SNA3|S000003687|Integral membrane protein localized to vacuolar intralumenal vesicles, computational analysis of large-scale protein-protein interaction data suggests a possible role in either cell wall synthesis or protein-vacuolar targeting
YBR085C-A	1.54544	MSN4	YBR085C-A||S000007522|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus
YJL068C	1.54526	MSN4	YJL068C||S000003604|Non-essential intracellular esterase that can function as an S-formylglutathione hydrolase; may be involved in the detoxification of formaldehyde, which can be metabolized to S-formylglutathione; similar to human esterase D
YPL261C	1.5426	MSN4	YPL261C||S000006182|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YPL260W
YFL053W	1.53811	MSN4	YFL053W|DAK2|S000001841|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YGR268C	1.52352	MSN4	YGR268C|HUA1|S000003500|Cytoplasmic protein containing a zinc finger domain with sequence similarity to that of Type I J-proteins; computational analysis of large-scale protein-protein interaction data suggests a possible role in actin patch assembly
YEL010W	1.52293	MSN4	YEL010W||S000000736|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR205C	1.51452	MSN4	YLR205C|HMX1|S000004195|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
YNL237W	1.51404	MSN4	YNL237W|YTP1|S000005181|Probable type-III integral membrane protein of unknown function, has regions of similarity to mitochondrial electron transport proteins
YAL018C	1.51345	MSN4	YAL018C||S000000016|Putative protein of unknown function
YJL042W	1.51042	MSN4	YJL042W|MHP1|S000003578|Microtubule-associated protein involved in assembly and stabilization of microtubules; overproduction results in cell cycle arrest at G2 phase; similar to Drosophila protein MAP and to mammalian MAP4 proteins
YNL160W	1.50254	MSN4	YNL160W|YGP1|S000005104|Cell wall-related secretory glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in adaptation prior to stationary phase entry; has similarity to Sps100p
YGR022C	1.50147	MSN4	YGR022C||S000003254|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps almost completely with the verified ORF MTL1/YGR023W
YLR124W	1.50029	MSN4	YLR124W||S000004114|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YKL043W	1.49927	MSN4	YKL043W|PHD1|S000001526|Transcriptional activator that enhances pseudohyphal growth; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate
YJL020C	1.49705	MSN4	YJL020C|BBC1|S000003557|Protein possibly involved in assembly of actin patches; interacts with an actin assembly factor Las17p and with the SH3 domains of Type I myosins Myo3p and Myo5p; localized predominantly to cortical actin patches
YPL222W	1.48918	MSN4	YPL222W|FMP40|S000006143|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGL205W	1.45722	MSN4	YGL205W|POX1|S000003173|Fatty-acyl coenzyme A oxidase, involved in the fatty acid beta-oxidation pathway; localized to the peroxisomal matrix
YDR476C	1.45596	MSN4	YDR476C||S000002884|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YDR476C is not an essential gene
YBR018C	1.45092	MSN4	YBR018C|GAL7|S000000222|Galactose-1-phosphate uridyl transferase, synthesizes glucose-1-phosphate and UDP-galactose from UDP-D-glucose and alpha-D-galactose-1-phosphate in the second step of galactose catabolism
YGR110W	1.44404	MSN4	YGR110W||S000003342|Putative protein of unknown function; transcription is increased in response to genotoxic stress; plays a role in restricting Ty1 transposition
YOR054C	1.44375	MSN4	YOR054C|VHS3|S000005580|Functionally redundant (see also SIS2) inhibitory subunit of Ppz1p, a PP1c-related ser/thr protein phosphatase Z isoform; synthetically lethal with sis2; putative phosphopantothenoylcysteine decarboxylase involved in coenzyme A biosynthesis
YOR081C	1.4428	MSN4	YOR081C|TGL5|S000005607|Triacylglycerol lipase involved in TAG mobilization; localizes to lipid particles; potential Cdc28p substrate
YDR255C	1.44223	MSN4	YDR255C|RMD5|S000002663|Cytosolic protein required for sporulation; also required for the ubiquitination of the gluconeogenetic enzyme fructose-1,6-bisphosphatase, which is degraded rapidly after the switch from gluconeogenesis to glycolysis
YCR025C	1.43184	MSN4	YCR025C||S000000620|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YCR025C is not an essential gene
YLR201C	1.43118	MSN4	YLR201C|COQ9|S000004191|Protein required for ubiquinone (coenzyme Q) biosynthesis and respiratory growth; localizes to the matrix face of the mitochondrial inner membrane in a large complex with ubiquinone biosynthetic enzymes
YER147C	1.43017	MSN4	YER147C|SCC4|S000000949|Subunit of cohesin loading factor (Scc2p-Scc4p), a complex required for the loading of cohesin complexes onto chromosomes; involved in establishing sister chromatid cohesion during double-strand break repair via phosphorylated histone H2AX
YJL052W	1.42593	MSN4	YJL052W|TDH1|S000003588|Glyceraldehyde-3-phosphate dehydrogenase, isozyme 1, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell-wall
YNL200C	1.42388	MSN4	YNL200C||S000005144|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHL046W-A	1.39578	MSN4	YHL046W-A||S000028775|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR284W	1.39165	MSN4	YBR284W||S000000488|Putative protein of unknown function; YBR284W is not an essential gene; null mutant exhibits decreased resistance to rapamycin and wortmannin
YML091C	1.38993	MSN4	YML091C|RPM2|S000004556|Protein subunit of mitochondrial RNase P, has roles in nuclear transcription, cytoplasmic and mitochondrial RNA processing, and mitochondrial translation; distributed to mitochondria, cytoplasmic processing bodies, and the nucleus
YFL020C	1.38697	MSN4	YFL020C|PAU5|S000001874|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
YKR102W	1.38327	MSN4	YKR102W|FLO10|S000001810|Lectin-like protein with similarity to Flo1p, thought to be involved in flocculation
YJL070C	1.37481	MSN4	YJL070C||S000003606|Putative protein of unknown function with similarity to AMP deaminases; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YJL070C is a non-essential gene
YLR125W	1.37199	MSN4	YLR125W||S000004115|Putative protein of unknown function; mutant has decreased Ty3 transposition; YLR125W is not an essential gene
YJR128W	1.368	MSN4	YJR128W||S000003889|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RSF2
YDR306C	1.35015	MSN4	YDR306C||S000002714|F-box protein of unknown function; interacts with Sgt1p via a Leucine-Rich Repeat (LRR) domain
YMR271C	1.34944	MSN4	YMR271C|URA10|S000004884|Minor orotate phosphoribosyltransferase (OPRTase) isozyme that catalyzes the fifth enzymatic step in the de novo biosynthesis of pyrimidines, converting orotate into orotidine-5'-phosphate; major OPRTase encoded by URA5
YPR061C	1.34896	MSN4	YPR061C|JID1|S000006265|Probable Hsp40p co-chaperone, has a DnaJ-like domain and appears to be involved in ER-associated degradation of misfolded proteins containing a tightly folded cytoplasmic domain; inhibits replication of Brome mosaic virus in S. cerevisiae
YDR533C	1.34821	MSN4	YDR533C|HSP31|S000002941|Possible chaperone and cysteine protease with similarity to E. coli Hsp31; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease; exists as a dimer and contains a putative metal-binding site
YJL149W	1.3392	MSN4	YJL149W|DAS1|S000003685|Putative SCF ubiquitin ligase F-box protein; interacts physically with both Cdc53p and Skp1 and genetically with CDC34; similar to putative F-box protein YDR131C; null mutant suppresses dst1delta sensitivity for 6-azauracil
YEL012W	1.33719	MSN4	YEL012W|UBC8|S000000738|Ubiquitin-conjugating enzyme that negatively regulates gluconeogenesis by mediating the glucose-induced ubiquitination of fructose-1,6-bisphosphatase (FBPase); cytoplasmic enzyme that catalyzes the ubiquitination of histones in vitro
YJR045C	1.33541	MSN4	YJR045C|SSC1|S000003806|Mitochondrial matrix ATPase, subunit of the presequence translocase-associated protein import motor (PAM) and of SceI endonuclease; involved in protein folding and translocation into the matrix; phosphorylated; member of HSP70 family
YGL227W	1.32703	MSN4	YGL227W|VID30|S000003196|Protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); shifts the balance of nitrogen metabolism toward the production of glutamate; localized to the nucleus and the cytoplasm
YNL015W	1.32526	MSN4	YNL015W|PBI2|S000004960|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
YJR046W	1.32299	MSN4	YJR046W|TAH11|S000003807|DNA replication licensing factor, required for pre-replication complex assembly
YOR055W	1.31936	MSN4	YOR055W||S000005581|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YDL197C	1.31872	MSN4	YDL197C|ASF2|S000002356|Anti-silencing protein that causes derepression of silent loci when overexpressed
YBR054W	1.31783	MSN4	YBR054W|YRO2|S000000258|Putative protein of unknown function; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies; transcriptionally regulated by Haa1p
YGL249W	1.3161	MSN4	YGL249W|ZIP2|S000003218|Meiosis-specific protein involved in normal synaptonemal complex formation and pairing between homologous chromosomes during meiosis
YBL047C	1.31587	MSN4	YBL047C|EDE1|S000000143|Key endocytic protein involved in a network of interactions with other endocytic proteins, binds membranes in a ubiquitin-dependent manner, may also bind ubiquitinated membrane-associated proteins
YNL142W	1.31584	MSN4	YNL142W|MEP2|S000005086|Ammonium permease involved in regulation of pseudohyphal growth; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation
YDR536W	1.31273	MSN4	YDR536W|STL1|S000002944|Glycerol proton symporter of the plasma membrane, subject to glucose-induced inactivation, strongly but transiently induced when cells are subjected to osmotic shock
YGR221C	1.31245	MSN4	YGR221C|TOS2|S000003453|Protein involved in localization of Cdc24p to the site of bud growth; may act as a membrane anchor; localizes to the bud neck and bud tip; potentially phosphorylated by Cdc28p
YDL124W	1.31237	MSN4	YDL124W||S000002282|NADPH-dependent alpha-keto amide reductase; reduces aromatic alpha-keto amides, aliphatic alpha-keto esters, and aromatic alpha-keto esters; member of the aldo-keto reductase (AKR) family
YOL129W	1.30593	MSN4	YOL129W|VPS68|S000005489|Vacuolar membrane protein of unknown function involved in vacuolar protein sorting; also detected in the mitochondria
YNL094W	1.29954	MSN4	YNL094W|APP1|S000005038|Protein of unknown function, interacts with Rvs161p and Rvs167p; computational analysis of protein-protein interactions in large-scale studies suggests a possible role in actin filament organization
YHR211W	1.2963	MSN4	YHR211W|FLO5|S000001254|Lectin-like cell wall protein (flocculin) involved in flocculation, binds to mannose chains on the surface of other cells, confers floc-forming ability that is chymotrypsin resistant but heat labile; similar to Flo1p
YJR147W	1.29331	MSN4	YJR147W|HMS2|S000003908|Protein with similarity to heat shock transcription factors; overexpression suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null mutant
YPR192W	1.28438	MSN4	YPR192W|AQY1|S000006396|Spore-specific water channel that mediates the transport of water across cell membranes, developmentally controlled; may play a role in spore maturation, probably by allowing water outflow, may be involved in freeze tolerance
YKL151C	1.28275	MSN4	YKL151C||S000001634|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YCR007C	1.28223	MSN4	YCR007C||S000000600|Putative integral membrane protein, member of DUP240 gene family; YCR007C is not an essential gene
YNL025C	1.28077	MSN4	YNL025C|SSN8|S000004970|Cyclin-like component of the RNA polymerase II holoenzyme, involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression and telomere maintenance
YIL047C	1.27868	MSN4	YIL047C|SYG1|S000001309|Plasma membrane protein of unknown function; truncation and overexpression suppresses lethality of G-alpha protein deficiency
YAL017W	1.26774	MSN4	YAL017W|PSK1|S000000015|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
YEL060C	1.26747	MSN4	YEL060C|PRB1|S000000786|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
YLR202C	1.2662	MSN4	YLR202C||S000004192|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF YLR201C; ORF contains a putative intron
YER116C	1.25946	MSN4	YER116C|SLX8|S000000918|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YDL244W	1.25853	MSN4	YDL244W|THI13|S000002403|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YHL047C	1.24308	MSN4	YHL047C|ARN2|S000001039|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
YBR230W-A	1.24237	MSN4	YBR230W-A||S000029722|Putative protein of unknown function
YAR023C	1.24005	MSN4	YAR023C||S000000074|Putative integral membrane protein, member of DUP240 gene family
YDL072C	1.23746	MSN4	YDL072C|YET3|S000002230|Protein of unknown function; YET3 null mutant decreases the level of secreted invertase; homolog of human BAP31 protein
YML042W	1.22704	MSN4	YML042W|CAT2|S000004506|Carnitine acetyl-CoA transferase present in both mitochondria and peroxisomes, transfers activated acetyl groups to carnitine to form acetylcarnitine which can be shuttled across membranes
YMR304W	1.22619	MSN4	YMR304W|UBP15|S000004920|Ubiquitin-specific protease that may play a role in ubiquitin precursor processing
YKL102C	1.22105	MSN4	YKL102C||S000001585|Dubious open reading frame unlikely to encode a functional protein; deletion confers sensitivity to citric acid; predicted protein would include a thiol-disulfide oxidoreductase active site
YGR149W	1.22068	MSN4	YGR149W||S000003381|Putative protein of unknown function; predicted to be an integal membrane protein
YGR008C	1.21862	MSN4	YGR008C|STF2|S000003240|Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p may act as stabilizing factors that enhance inhibitory action of the Inh1p protein
YCL065W	1.21808	MSN4	YCL065W||S000000570|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps HMLALPHA1
YGL215W	1.21129	MSN4	YGL215W|CLG1|S000003183|Cyclin-like protein that interacts with Pho85p; has sequence similarity to G1 cyclins PCL1 and PCL2
YLR053C	1.2028	MSN4	YLR053C||S000004043|Putative protein of unknown function
YDR542W	1.19851	MSN4	YDR542W|PAU10|S000002950|Hypothetical protein
YHR080C	1.19809	MSN4	YHR080C||S000001122|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR436W	1.19242	MSN4	YDR436W|PPZ2|S000002844|Serine/threonine protein phosphatase Z, isoform of Ppz1p; involved in regulation of potassium transport, which affects osmotic stability, cell cycle progression, and halotolerance
YNR014W	1.19127	MSN4	YNR014W||S000005297|Putative protein of unknown function; expression is cell-cycle regulated, Azf1p-dependent, and heat-inducible
YOR227W	1.18473	MSN4	YOR227W||S000005753|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YCL052C	1.18297	MSN4	YCL052C|PBN1|S000000557|Essential component of glycosylphosphatidylinositol-mannosyltransferase I, required for the autocatalytic post-translational processing of the protease B precursor Prb1p, localizes to ER in lumenal orientation; homolog of mammalian PIG-X
YER053C	1.16206	MSN4	YER053C|PIC2|S000000855|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
YEL007W	1.15778	MSN4	YEL007W||S000000733|Putative protein with sequence similarity to S. pombe gti1+ (gluconate transport inducer 1)
YPL154C	1.15227	MSN4	YPL154C|PEP4|S000006075|Vacuolar aspartyl protease (proteinase A), required for the posttranslational precursor maturation of vacuolar proteinases; important for protein turnover after oxidative damage; synthesized as a zymogen, self-activates
YJR127C	1.15108	MSN4	YJR127C|RSF2|S000003888|Zinc-finger protein involved in transcriptional control of both nuclear and mitochondrial genes, many of which specify products required for glycerol-based growth, respiration, and other functions
YMR170C	1.12621	MSN4	YMR170C|ALD2|S000004780|Cytoplasmic aldehyde dehydrogenase, involved in ethanol oxidation and beta-alanine biosynthesis; uses NAD+ as the preferred coenzyme; expression is stress induced and glucose repressed; very similar to Ald3p
YML004C	1.12385	MSN4	YML004C|GLO1|S000004463|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
YIL166C	1.11445	MSN4	YIL166C||S000001428|Putative protein with similarity to the allantoate permease (Dal5p) subfamily of the major facilitator superfamily; mRNA expression is elevated by sulfur limitation; YIL166C is a non-essential gene
YOR386W	1.11337	MSN4	YOR386W|PHR1|S000005913|DNA photolyase involved in photoreactivation, repairs pyrimidine dimers in the presence of visible light; induced by DNA damage; regulated by transcriptional repressor Rph1p
YML132W	1.1101	MSN4	YML132W|COS3|S000004601|Protein involved in salt resistance; interacts with sodium:hydrogen antiporter Nha1p; member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YJL038C	1.10851	MSN4	YJL038C|LOH1|S000003575|Putative protein of unknown function; expression induced during sporulation and repressed during vegetative growth by Sum1p and Hst1p; similar to adjacent open reading frame, YJL037W
YOR290C	1.10797	MSN4	YOR290C|SNF2|S000005816|Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; contains DNA-stimulated ATPase activity; functions interdependently in transcriptional activation with Snf5p and Snf6p
YMR165C	1.10778	MSN4	YMR165C|PAH1|S000004775|Mg2+-dependent phosphatidate (PA) phosphatase, catalyzes the dephosphorylation of PA to yield diacylglycerol and Pi, responsible for de novo lipid synthesis; homologous to mammalian lipin 1
YPL061W	1.10285	MSN4	YPL061W|ALD6|S000005982|Cytosolic aldehyde dehydrogenase, activated by Mg2+ and utilizes NADP+ as the preferred coenzyme; required for conversion of acetaldehyde to acetate; constitutively expressed; locates to the mitochondrial outer surface upon oxidative stress
YGR102C	1.10166	MSN4	YGR102C||S000003334|Putative protein of unknown function; transposon insertion mutant is salt sensitive and deletion mutant has growth defects; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPL260W	1.10137	MSN4	YPL260W||S000006181|Putative substrate of cAMP-dependent protein kinase (PKA); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YPL260W is not an essential gene
YLR064W	1.10103	MSN4	YLR064W||S000004054|Putative protein of unknown function; highly conserved across species and orthologous to human TMEM33; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YLR064W is not an essential gene
YNL115C	1.0963	MSN4	YNL115C||S000005059|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YNL115C is not an essential gene
YHR009C	1.09586	MSN4	YHR009C||S000001051|Putative protein of unknown function; not an essential gene
YMR216C	1.0944	MSN4	YMR216C|SKY1|S000004829|SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1
YNL036W	1.08887	MSN4	YNL036W|NCE103|S000004981|Carbonic anhydrase; poorly transcribed under aerobic conditions and at an undetectable level under anaerobic conditions; involved in non-classical protein export pathway
YDR334W	1.08053	MSN4	YDR334W|SWR1|S000002742|Swi2/Snf2-related ATPase that is the structural component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A
YMR272C	1.07758	MSN4	YMR272C|SCS7|S000004885|Sphingolipid alpha-hydroxylase, functions in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids, has both cytochrome b5-like and hydroxylase/desaturase domains, not essential for growth
YGR254W	1.07725	MSN4	YGR254W|ENO1|S000003486|Enolase I, a phosphopyruvate hydratase that catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate during glycolysis and the reverse reaction during gluconeogenesis; expression is repressed in response to glucose
YPL222C-A	1.07708	MSN4	YPL222C-A||S000028722|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YJR121W	1.07423	MSN4	YJR121W|ATP2|S000003882|Beta subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YGL208W	1.07285	MSN4	YGL208W|SIP2|S000003176|One of three beta subunits of the Snf1 serine/threonine protein kinase complex involved in the response to glucose starvation; null mutants exhibit accelerated aging; N-myristoylprotein localized to the cytoplasm and the plasma membrane
YOL128C	1.06947	MSN4	YOL128C|YGK3|S000005488|Protein kinase related to mammalian glycogen synthase kinases of the GSK-3 family; GSK-3 homologs (Mck1p, Rim11p, Mrk1p, Ygk3p) are involved in control of Msn2p-dependent transcription of stress responsive genes and in protein degradation
YLR111W	1.0684	MSN4	YLR111W||S000004101|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YFR033C	1.06804	MSN4	YFR033C|QCR6|S000001929|Subunit 6 of the ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; highly acidic protein; required for maturation of cytochrome c1
YDL138W	1.06237	MSN4	YDL138W|RGT2|S000002297|Plasma membrane glucose receptor, highly similar to Snf3p; both Rgt2p and Snf3p serve as transmembrane glucose sensors generating an intracellular signal that induces expression of glucose transporter (HXT) genes
YDR479C	1.05816	MSN4	YDR479C|PEX29|S000002887|Peroxisomal integral membrane peroxin, involved in the regulation of peroxisomal size, number and distribution; genetic interactions suggest that Pex28p and Pex29p act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p
YKR058W	1.05757	MSN4	YKR058W|GLG1|S000001766|Self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian glycogenin
YLR233C	1.05738	MSN4	YLR233C|EST1|S000004223|TLC1 RNA-associated factor involved in telomere length regulation as the recruitment subunit of the telomerase holoenzyme, has a possible role in activating Est2p-TLC1-RNA bound to the telomere
YGR281W	1.05628	MSN4	YGR281W|YOR1|S000003513|Plasma membrane ATP-binding cassette (ABC) transporter, multidrug transporter mediates export of many different organic anions including oligomycin
YOR291W	1.05598	MSN4	YOR291W||S000005817|Putative protein of unknown function; shares sequence similarity with the type V P-type ATPase Spf1p; YOR291W is not an essential protein
YOR134W	1.05107	MSN4	YOR134W|BAG7|S000005660|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
YOL117W	1.04986	MSN4	YOL117W|RRI2|S000005477|Subunit of the COP9 signalosome (CSN) complex that cleaves the ubiquitin-like protein Nedd8 from SCF ubiquitin ligases; plays a role in the mating pheromone response
YGL183C	1.04572	MSN4	YGL183C|MND1|S000003151|Protein required for recombination and meiotic nuclear division; forms a complex with Hop2p, which is involved in chromosome pairing and repair of meiotic double-strand breaks
YMR092C	1.04146	MSN4	YMR092C|AIP1|S000004698|Actin cortical patch component, interacts with the actin depolymerizing factor cofilin; required to restrict cofilin localization to cortical patches; contains WD repeats
YLR297W	1.04056	MSN4	YLR297W||S000004288|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YLR297W is not an essential gene; induced by treatment with 8-methoxypsoralen and UVA irradiation
YLR228C	1.03893	MSN4	YLR228C|ECM22|S000004218|Sterol regulatory element binding protein, regulates transcription of the sterol biosynthetic genes ERG2 and ERG3; member of the fungus-specific Zn[2]-Cys[6] binuclear cluster family of transcription factors; homologous to Upc2p
YHR071W	1.02576	MSN4	YHR071W|PCL5|S000001113|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
YAL063C	1.02479	MSN4	YAL063C|FLO9|S000000059|Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation
YGR260W	1.01283	MSN4	YGR260W|TNA1|S000003492|High affinity nicotinic acid plasma membrane permease, responsible for uptake of low levels of nicotinic acid; expression of the gene increases in the absence of extracellular nicotinic acid or para-aminobenzoate (PABA)
YDR391C	1.00629	MSN4	YDR391C||S000002799|Putative protein of unknown function, possibly involved in zinc homeostasis; Bdf1p-dependent transcription induced by salt stress; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YNL321W	1.00606	MSN4	YNL321W|VNX1|S000005265|Low affinity vacuolar membrane localized monovalent cation/H+ antiporter; member of the calcium exchanger (CAX) family; potential Cdc28p substrate
YCR083W	1.00426	MSN4	YCR083W|TRX3|S000000679|Mitochondrial thioredoxin, highly conserved oxidoreductase required to maintain the redox homeostasis of the cell, forms the mitochondrial thioredoxin system with Trr2p, redox state is maintained by both Trr2p and Glr1p
YLL039C	1.00288	MSN4	YLL039C|UBI4|S000003962|Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats
YOL081W	0.992432	MSN4	YOL081W|IRA2|S000005441|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, has similarity to Ira1p and human neurofibromin
YJR152W	0.98713	MSN4	YJR152W|DAL5|S000003913|Allantoin permease; ureidosuccinate permease; expression is constitutive but sensitive to nitrogen catabolite repression
YPR015C	0.985979	MSN4	YPR015C||S000006219|Putative protein of unknown function
YJL199C	0.984691	MSN4	YJL199C|MBB1|S000003735|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies
YPR193C	0.983725	MSN4	YPR193C|HPA2|S000006397|Tetrameric histone acetyltransferase with similarity to Gcn5p, Hat1p, Elp3p, and Hpa3p; acetylates histones H3 and H4 in vitro and exhibits autoacetylation activity
YJL163C	0.982343	MSN4	YJL163C||S000003699|Putative protein of unknown function
YGL248W	0.981255	MSN4	YGL248W|PDE1|S000003217|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
YDR231C	0.980633	MSN4	YDR231C|COX20|S000002639|Mitochondrial inner membrane protein, required for proteolytic processing of Cox2p and its assembly into cytochrome c oxidase
YIL065C	0.979813	MSN4	YIL065C|FIS1|S000001327|Mitochondrial outer membrane protein involved in membrane fission, required for localization of Dnm1p and Mdv1p during mitochondrial division; mediates ethanol-induced apoptosis and ethanol-induced mitochondrial fragmentation
YPL224C	0.972483	MSN4	YPL224C|MMT2|S000006145|Putative metal transporter involved in mitochondrial iron accumulation; closely related to Mmt1p
YPL183W-A	0.971248	MSN4	YPL183W-A|RTC6|S000007224|Homolog of the prokaryotic ribosomal protein L36, likely to be a mitochondrial ribosomal protein coded in the nuclear genome; null mutation suppresses cdc13-1 temperature sensitivity
YOL048C	0.965896	MSN4	YOL048C||S000005408|Putative protein of unknown function
YLR164W	0.963526	MSN4	YLR164W||S000004154|Mitochondrial inner membrane of unknown function; similar to Tim18p and Sdh4p; expression induced by nitrogen limitation in a GLN3, GAT1-dependent manner
YLR402W	0.960651	MSN4	YLR402W||S000004394|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR208W	0.960164	MSN4	YOR208W|PTP2|S000005734|Phosphotyrosine-specific protein phosphatase involved in the inactivation of mitogen-activated protein kinase (MAPK) during osmolarity sensing; dephosporylates Hog1p MAPK and regulates its localization; localized to the nucleus
YBL099W	0.958643	MSN4	YBL099W|ATP1|S000000195|Alpha subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YDL149W	0.957137	MSN4	YDL149W|ATG9|S000002308|Transmembrane protein involved in formation of Cvt and autophagic vesicles; cycles between the pre-autophagosomal structure and other cytosolic punctate structures, not found in autophagosomes; forms a complex with Atg23p and Atg27p
YBL017C	0.955626	MSN4	YBL017C|PEP1|S000000113|Type I transmembrane sorting receptor for multiple vacuolar hydrolases; cycles between the late-Golgi and prevacuolar endosome-like compartments
YPR172W	0.950587	MSN4	YPR172W||S000006376|Protein of unknown function, transcriptionally activated by Yrm1p along with genes involved in multidrug resistance
YOR053W	0.946419	MSN4	YOR053W||S000005579|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene VHS3/YOR054C
YDR541C	0.942875	MSN4	YDR541C||S000002949|Putative dihydrokaempferol 4-reductase
YDL218W	0.935664	MSN4	YDL218W||S000002377|Putative protein of unknown function; YDL218W transcription is regulated by Azf1p and induced by starvation and aerobic conditions
YDL147W	0.934908	MSN4	YDL147W|RPN5|S000002306|Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p
YIL046W	0.933636	MSN4	YIL046W|MET30|S000001308|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
YEL072W	0.929926	MSN4	YEL072W|RMD6|S000000798|Protein required for sporulation
YCR023C	0.925562	MSN4	YCR023C||S000000617|Vacuolar membrane protein of unknown function; member of the multidrug resistance family; YCR023C is not an essential gene
YNL125C	0.924992	MSN4	YNL125C|ESBP6|S000005069|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
YKL032C	0.923815	MSN4	YKL032C|IXR1|S000001515|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
YPL203W	0.92347	MSN4	YPL203W|TPK2|S000006124|cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p
YPL109C	0.921401	MSN4	YPL109C||S000006030|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR403W	0.919541	MSN4	YLR403W|SFP1|S000004395|Transcription factor that controls expression of many ribosome biogenesis genes in response to nutrients and stress, regulates G2/M transitions during mitotic cell cycle and DNA-damage response, involved in cell size modulation
YNL095C	0.915527	MSN4	YNL095C||S000005039|Putative protein of unknown function predicted to contain a transmembrane domain; YNL095C is not an essential gene
YHR078W	0.914777	MSN4	YHR078W||S000001120|High osmolarity-regulated gene of unknown function
YER125W	0.913367	MSN4	YER125W|RSP5|S000000927|Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain
YHR180W	0.912444	MSN4	YHR180W||S000001223|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJL133C-A	0.912148	MSN4	YJL133C-A||S000028805|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHR082C	0.909978	MSN4	YHR082C|KSP1|S000001124|Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation
YKL142W	0.909742	MSN4	YKL142W|MRP8|S000001625|Putative mitochondrial ribosomal protein, has similarity to E. coli ribosomal protein S2
YJL220W	0.908961	MSN4	YJL220W||S000003756|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YJL221C/FSP2
YMR139W	0.908055	MSN4	YMR139W|RIM11|S000004747|Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta
YHL025W	0.90776	MSN4	YHL025W|SNF6|S000001017|Subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2p and Snf5p
YOR062C	0.905173	MSN4	YOR062C||S000005588|Protein of unknown function; similar to YKR075Cp and Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YLR234W	0.895142	MSN4	YLR234W|TOP3|S000004224|DNA Topoisomerase III, conserved protein that functions in a complex with Sgs1p and Rmi1p to relax single-stranded negatively-supercoiled DNA preferentially, involved in telomere stability and regulation of mitotic recombination
YGR286C	0.891841	MSN4	YGR286C|BIO2|S000003518|Biotin synthase, catalyzes the conversion of dethiobiotin to biotin, which is the last step of the biotin biosynthesis pathway; complements E. coli bioB mutant
YKL150W	0.886846	MSN4	YKL150W|MCR1|S000001633|Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis
YGR068C	0.886181	MSN4	YGR068C||S000003300|Putative protein of unknown function; YGR068C is not an essential gene.
YDR446W	0.884709	MSN4	YDR446W|ECM11|S000002854|Non-essential protein apparently involved in meiosis, GFP fusion protein is present in discrete clusters in the nucleus throughout mitosis; may be involved in maintaining chromatin structure
YKL065W-A	0.884529	MSN4	YKL065W-A||S000113563|Putative protein of unknown function
YNL274C	0.88241	MSN4	YNL274C|GOR1|S000005218|Glyoxylate reductase; null mutation results in increased biomass after diauxic shift; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPR023C	0.879894	MSN4	YPR023C|EAF3|S000006227|Esa1p-associated factor, nonessential component of the NuA4 acetyltransferase complex, homologous to Drosophila dosage compensation protein MSL3; plays a role in regulating Ty1 transposition
YGL170C	0.877791	MSN4	YGL170C|SPO74|S000003138|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
YPR149W	0.869223	MSN4	YPR149W|NCE102|S000006353|Protein of unknown function; contains transmembrane domains; involved in secretion of proteins that lack classical secretory signal sequences; component of the detergent-insoluble glycolipid-enriched complexes (DIGs)
YGL198W	0.865112	MSN4	YGL198W|YIP4|S000003166|Protein that interacts with Rab GTPases, localized to late Golgi vesicles; computational analysis of large-scale protein-protein interaction data suggests a possible role in vesicle-mediated transport
YLL049W	0.859619	MSN4	YLL049W|LDB18|S000003972|Protein of unknown function; null mutant shows a reduced affinity for the alcian blue dye suggesting a decreased net negative charge of the cell surface
YJR021C	0.85347	MSN4	YJR021C|REC107|S000003782|Protein involved in early stages of meiotic recombination; involved in coordination between the initiation of recombination and the first division of meiosis; part of a complex (Rec107p-Mei4p-Rec114p) required for ds break formation
YJL019W	0.840239	MSN4	YJL019W|MPS3|S000003556|Essential integral membrane protein required for spindle pole body duplication and for nuclear fusion, localizes to the spindle pole body half bridge, interacts with DnaJ-like chaperone Jem1p and with centrin homolog Cdc31p
YMR013C	0.840169	MSN4	YMR013C|SEC59|S000004615|Dolichol kinase, catalyzes the terminal step in dolichyl monophosphate (Dol-P) biosynthesis; required for viability and for normal rates of lipid intermediate synthesis and protein N-glycosylation
YPR127W	0.839792	MSN4	YPR127W||S000006331|Putative protein of unknown function; expression is activated by transcription factor YRM1/YOR172W; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YFL036W	0.836305	MSN4	YFL036W|RPO41|S000001858|Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; requires a specificity subunit encoded by MTF1 for promoter recognition
YBR077C	0.833721	MSN4	YBR077C|SLM4|S000000281|Component of the EGO complex, which is involved in the regulation of microautophagy, and of the GSE complex, which is required for proper sorting of amino acid permease Gap1p; gene exhibits synthetic genetic interaction with MSS4
YER066C-A	0.833188	MSN4	YER066C-A||S000002959|Dubious open reading frame unlikely to encode a protein, partially overlaps uncharacterized ORF YER067W
YML133C	0.832723	MSN4	YML133C||S000004602|Putative protein of unknown function with similarity to helicases; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YML133C contains an intron
YNL006W	0.830713	MSN4	YNL006W|LST8|S000004951|Protein required for the transport of amino acid permease Gap1p from the Golgi to the cell surface; component of the TOR signaling pathway; associates with both Tor1p and Tor2p; contains a WD-repeat
YDR443C	0.830403	MSN4	YDR443C|SSN2|S000002851|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for stable association of Srb10p-Srb11p kinase; essential for transcriptional regulation
YNL283C	0.828265	MSN4	YNL283C|WSC2|S000005227|Partially redundant sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway involved in maintenance of cell wall integrity and recovery from heat shock; secretory pathway Wsc2p is required for the arrest of secretion response
YPR145C-A	0.823182	MSN4	YPR145C-A||S000113589|Putative protein of unknown function
YNL063W	0.82193	MSN4	YNL063W|MTQ1|S000005007|S-adenosylmethionine-dependent methyltransferase; methylates translational release factor Mrf1p; similar to E.coli PrmC; is not an essential gene
YMR257C	0.819978	MSN4	YMR257C|PET111|S000004870|Mitochondrial translational activator specific for the COX2 mRNA; located in the mitochondrial inner membrane
YFR049W	0.817577	MSN4	YFR049W|YMR31|S000001945|Mitochondrial ribosomal protein of the small subunit, has similarity to human mitochondrial ribosomal protein MRP-S36
YNL011C	0.817185	MSN4	YNL011C||S000004956|Putative protein of unknown function; YNL011C is not an essential gene
YPL013C	0.8158	MSN4	YPL013C|MRPS16|S000005934|Mitochondrial ribosomal protein of the small subunit
YDR358W	0.814713	MSN4	YDR358W|GGA1|S000002766|Golgi-localized protein with homology to gamma-adaptin, interacts with and regulates Arf1p and Arf2p in a GTP-dependent manner in order to facilitate traffic through the late Golgi
YDR505C	0.814241	MSN4	YDR505C|PSP1|S000002913|Asn and gln rich protein of unknown function; high-copy suppressor of POL1 (DNA polymerase alpha) and partial suppressor of CDC2 (polymerase delta) and CDC6 (pre-RC loading factor) mutations; overexpression results in growth inhibition
YGR059W	0.808605	MSN4	YGR059W|SPR3|S000003291|Sporulation-specific homolog of the yeast CDC3/10/11/12 family of bud neck microfilament genes; septin protein involved in sporulation; regulated by ABFI
YPL015C	0.807627	MSN4	YPL015C|HST2|S000005936|Cytoplasmic member of the silencing information regulator 2 (Sir2) family of NAD(+)-dependent protein deacetylases; modulates nucleolar (rDNA) and telomeric silencing; possesses NAD(+)-dependent histone deacetylase activity in vitro
YCR073W-A	0.806893	MSN4	YCR073W-A|SOL2|S000000718|Protein with a possible role in tRNA export; shows similarity to 6-phosphogluconolactonase non-catalytic domains but does not exhibit this enzymatic activity; homologous to Sol1p, Sol3p, and Sol4p
YGL062W	0.806797	MSN4	YGL062W|PYC1|S000003030|Pyruvate carboxylase isoform, cytoplasmic enzyme that converts pyruvate to oxaloacetate; highly similar to isoform Pyc2p but differentially regulated; mutations in the human homolog are associated with lactic acidosis
YMR291W	0.805243	MSN4	YMR291W||S000004905|Putative kinase of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YMR291W is not an essential gene
YNL157W	0.802206	MSN4	YNL157W|IGO1|S000005101|Hypothetical protein
YOR010C	0.801915	MSN4	YOR010C|TIR2|S000005536|Putative cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins; transcription is induced by cold shock and anaerobiosis
YEL030C-A	0.801844	MSN4	YEL030C-A||S000028619|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YGR053C	0.801268	MSN4	YGR053C||S000003285|Putative protein of unknown function
YIR014W	0.800976	MSN4	YIR014W||S000001453|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR014W is a non-essential gene
YDR022C	0.800864	MSN4	YDR022C|CIS1|S000002429|Autophagy-specific protein required for autophagosome formation; may form a complex with Atg17p and Atg29p that localizes other proteins to the pre-autophagosomal structure; high-copy suppressor of CIK1 deletion
YHR016C	0.79785	MSN4	YHR016C|YSC84|S000001058|Protein involved in the organization of the actin cytoskeleton; contains SH3 domain similar to Rvs167p
YJL221C	0.7969	MSN4	YJL221C|FSP2|S000003757|Protein of unknown function, expression is induced during nitrogen limitation
YGL255W	0.79348	MSN4	YGL255W|ZRT1|S000003224|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
YPL057C	0.792093	MSN4	YPL057C|SUR1|S000005978|Probable catalytic subunit of a mannosylinositol phosphorylceramide (MIPC) synthase, forms a complex with probable regulatory subunit Csg2p; function in sphingolipid biosynthesis is overlapping with that of Csh1p
YNL336W	0.792053	MSN4	YNL336W|COS1|S000005280|Protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YDR453C	0.790334	MSN4	YDR453C|TSA2|S000002861|Stress inducible cytoplasmic thioredoxin peroxidase; cooperates with Tsa1p in the removal of reactive oxygen, nitrogen and sulfur species using thioredoxin as hydrogen donor; deletion enhances the mutator phenotype of tsa1 mutants
YGR238C	0.785654	MSN4	YGR238C|KEL2|S000003470|Protein that functions in a complex with Kel1p to negatively regulate mitotic exit, interacts with Tem1p and Lte1p; localizes to regions of polarized growth; potential Cdc28p substrate
YDR466W	0.783632	MSN4	YDR466W|PKH3|S000002874|Protein kinase with similarity to mammalian phosphoinositide-dependent kinase 1 (PDK1) and yeast Pkh1p and Pkh2p, two redundant upstream activators of Pkc1p; identified as a multicopy suppressor of a pkh1 pkh2 double mutant
YDR406W	0.778985	MSN4	YDR406W|PDR15|S000002814|Plasma membrane ATP binding cassette (ABC) transporter, multidrug transporter and general stress response factor implicated in cellular detoxification; regulated by Pdr1p, Pdr3p and Pdr8p; promoter contains a PDR responsive element
YMR042W	0.777735	MSN4	YMR042W|ARG80|S000004645|Transcription factor involved in regulation of arginine-responsive genes; acts with Arg81p and Arg82p
YPL278C	0.776998	MSN4	YPL278C||S000006199|Putative protein of unknown function; gene expression regulated by copper levels
YNL143C	0.76949	MSN4	YNL143C||S000005087|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOL055C	0.767309	MSN4	YOL055C|THI20|S000005416|Multifunctional protein with both hydroxymethylpyrimidine kinase and thiaminase activities; involved in thiamine biosynthesis and also in thiamine degradation; member of a gene family with THI21 and THI22; functionally redundant with Thi21p
YMR041C	0.764144	MSN4	YMR041C|ARA2|S000004644|NAD-dependent arabinose dehydrogenase, involved in biosynthesis of erythroascorbic acid; similar to plant L-galactose dehydrogenase
YGR121C	0.763807	MSN4	YGR121C|MEP1|S000003353|Ammonium permease; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation
YPL258C	0.763776	MSN4	YPL258C|THI21|S000006179|Hydroxymethylpyrimidine phosphate kinase, involved in the last steps in thiamine biosynthesis; member of a gene family with THI20 and THI22; functionally redundant with Thi20p
YHL041W	0.76153	MSN4	YHL041W||S000001033|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YDL146W	0.75524	MSN4	YDL146W|LDB17|S000002305|Protein of unknown function; GFP-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; null mutant shows a reduced affinity for the alcian blue dye suggesting a decreased net negative charge of the cell surface
YDR333C	0.748588	MSN4	YDR333C||S000002741|Putative protein of unknown function
YLR037C	0.746329	MSN4	YLR037C|DAN2|S000004027|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YGL006W	0.744266	MSN4	YGL006W|PMC1|S000002974|Vacuolar Ca2+ ATPase involved in depleting cytosol of Ca2+ ions; prevents growth inhibition by activation of calcineurin in the presence of elevated concentrations of calcium; similar to mammalian PMCA1a
YLR395C	0.741761	MSN4	YLR395C|COX8|S000004387|Subunit VIII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YDL168W	0.740909	MSN4	YDL168W|SFA1|S000002327|Bifunctional enzyme containing both alcohol dehydrogenase and glutathione-dependent formaldehyde dehydrogenase activities, functions in formaldehyde detoxification and formation of long chain and complex alcohols, regulated by Hog1p-Sko1p
YNL241C	0.733902	MSN4	YNL241C|ZWF1|S000005185|Glucose-6-phosphate dehydrogenase (G6PD), catalyzes the first step of the pentose phosphate pathway; involved in adapting to oxidatve stress; homolog of the human G6PD which is deficient in patients with hemolytic anemia
YGR032W	0.733015	MSN4	YGR032W|GSC2|S000003264|Catalytic subunit of 1,3-beta-glucan synthase, involved in formation of the inner layer of the spore wall; activity positively regulated by Rho1p and negatively by Smk1p; has similarity to an alternate catalytic subunit, Fks1p (Gsc1p)
YMR148W	0.731461	MSN4	YMR148W||S000004756|Putative protein of unknown function; predicted to contain a transmembrane domain; YMR148W is not an essential gene
YJL135W	0.725758	MSN4	YJL135W||S000003671|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified genes YJL134W/LCB3
YGR127W	0.725108	MSN4	YGR127W||S000003359|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p, indicating a possible role in stress response
YCL056C	0.719823	MSN4	YCL056C||S000000561|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YJL057C	0.719426	MSN4	YJL057C|IKS1|S000003593|Putative serine/threonine kinase; expression is induced during mild heat stress; deletion mutants are hypersensitive to copper sulphate and resistant to sorbate; interacts with an N-terminal fragment of Sst2p
YDR232W	0.719383	MSN4	YDR232W|HEM1|S000002640|5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p
YHL008C	0.71897	MSN4	YHL008C||S000001000|Putative protein of unknown function, does not appear to be involved in monocarboxylic acid transport; green fluorescent protein (GFP)-fusion protein localizes to the vacuole
YHL026C	0.715992	MSN4	YHL026C||S000001018|Putative protein of unknown function; YHL026C is not an essential gene; in 2005 the start site was moved 141 nt upstream (see Locus History)
YJL159W	0.714639	MSN4	YJL159W|HSP150|S000003695|O-mannosylated heat shock protein that is secreted and covalently attached to the cell wall via beta-1,3-glucan and disulfide bridges; required for cell wall stability; induced by heat shock, oxidative stress, and nitrogen limitation
YDR319C	0.713957	MSN4	YDR319C|YFT2|S000002727|Putative protein of unknown function, identified as an ortholog of the highly conserved FIT family of proteins involved in triglyceride droplet biosynthesis; interacts with Sst2p and Hsp82p in high-throughput two-hybrid screens
YNL042W	0.712148	MSN4	YNL042W|BOP3|S000004987|Protein of unknown function, potential Cdc28p substrate; overproduction suppresses a pam1 slv3 double null mutation and confers resistance to methylmercury
YKR018C	0.698096	MSN4	YKR018C||S000001726|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YDL223C	0.697943	MSN4	YDL223C|HBT1|S000002382|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
YIL160C	0.697445	MSN4	YIL160C|POT1|S000001422|3-ketoacyl-CoA thiolase with broad chain length specificity, cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA during beta-oxidation of fatty acids
YDL243C	0.696528	MSN4	YDL243C|AAD4|S000002402|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase, involved in the oxidative stress response
YCL001W-B	0.688414	MSN4	YCL001W-B||S000007596|Putative protein of unknown function; identified by homology
YDL114W	0.686342	MSN4	YDL114W||S000002272|Putative protein of unknown function with similarity to acyl-carrier-protein reductases; YDL114W is not an essential gene
YNL009W	0.685259	MSN4	YNL009W|IDP3|S000004954|Peroxisomal NADP-dependent isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate with the formation of NADP(H+), required for growth on unsaturated fatty acids
YFR029W	0.679376	MSN4	YFR029W|PTR3|S000001925|Component of the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p), which senses external amino acid concentration and transmits intracellular signals that result in regulation of expression of amino acid permease genes
YFL029C	0.6784	MSN4	YFL029C|CAK1|S000001865|Cyclin-dependent kinase-activating kinase required for passage through the cell cycle, phosphorylates and activates Cdc28p; nucleotide-binding pocket differs significantly from those of most other protein kinases
YOR245C	0.669465	MSN4	YOR245C|DGA1|S000005771|Diacylglycerol acyltransferase, catalyzes the terminal step of triacylglycerol (TAG) formation, acylates diacylglycerol using acyl-CoA as an acyl donor, localized to lipid particles
YDL110C	0.668358	MSN4	YDL110C|TMA17|S000002268|Protein of unknown function that associates with ribosomes
YBR067C	0.668266	MSN4	YBR067C|TIP1|S000000271|Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat- and cold-shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins
YLR273C	0.665345	MSN4	YLR273C|PIG1|S000004263|Putative targeting subunit for the type-1 protein phosphatase Glc7p that tethers it to the Gsy2p glycogen synthase
YDR173C	0.661513	MSN4	YDR173C|ARG82|S000002580|Inositol polyphosphate multikinase (IPMK), sequentially phosphorylates Ins(1,4,5)P3 to form Ins(1,3,4,5,6)P5; also has diphosphoinositol polyphosphate synthase activity; regulates arginine-, phosphate-, and nitrogen-responsive genes
YOR351C	0.652125	MSN4	YOR351C|MEK1|S000005878|Meiosis-specific serine/threonine protein kinase, functions in meiotic checkpoint, promotes recombination between homologous chromosomes by suppressing double strand break repair between sister chromatids
YLR438W	0.651733	MSN4	YLR438W|CAR2|S000004430|L-ornithine transaminase (OTAse), catalyzes the second step of arginine degradation, expression is dually-regulated by allophanate induction and a specific arginine induction process; not nitrogen catabolite repression sensitive
YDR360W	0.646577	MSN4	YDR360W|OPI7|S000002768|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene VID21/YDR359C.
YDR216W	0.640277	MSN4	YDR216W|ADR1|S000002624|Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization
YJL219W	0.638248	MSN4	YJL219W|HXT9|S000003755|Putative hexose transporter that is nearly identical to Hxt11p, has similarity to major facilitator superfamily (MFS) transporters, expression of HXT9 is regulated by transcription factors Pdr1p and Pdr3p
YGL237C	0.637906	MSN4	YGL237C|HAP2|S000003206|Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; contains sequences sufficient for both complex assembly and DNA binding
YDL156W	0.637613	MSN4	YDL156W||S000002315|Putative protein of unknown function; protein sequence contains three WD domains (WD-40 repeat); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YLR334C	0.635856	MSN4	YLR334C||S000004326|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps a stand-alone long terminal repeat sequence whose presence indicates a retrotransposition event occurred here
YEL050C	0.633931	MSN4	YEL050C|RML2|S000000776|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
YAL008W	0.632881	MSN4	YAL008W|FUN14|S000000006|Mitochondrial protein of unknown function
YMR258C	0.632764	MSN4	YMR258C||S000004871|Protein of unknown function with similarity to F-box proteins; physically interacts with Skp1p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YMR258C is not an essential gene
YFL024C	0.632209	MSN4	YFL024C|EPL1|S000001870|Component of NuA4, which is an essential histone H4/H2A acetyltransferase complex; homologous to Drosophila Enhancer of Polycomb
YNR033W	0.631718	MSN4	YNR033W|ABZ1|S000005316|Para-aminobenzoate (PABA) synthase, has similarity to Escherichia coli PABA synthase components PabA and PabB
YDR528W	0.627487	MSN4	YDR528W|HLR1|S000002936|Protein involved in regulation of cell wall composition and integrity and response to osmotic stress; overproduction suppresses a lysis sensitive PKC mutation; similar to Lre1p, which functions antagonistically to protein kinase A
YLR345W	0.626637	MSN4	YLR345W||S000004337|Similar to 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase enzymes responsible for the metabolism of fructoso-2,6-bisphosphate; mRNA expression is repressed by the Rfx1p-Tup1p-Ssn6p repressor complex; YLR345W is not an essential gene
YHR210C	0.626248	MSN4	YHR210C||S000001253|Putative protein of unknown function; non-essential gene; highly expressed under anaeorbic conditions; sequence similarity to aldose 1-epimerases such as GAL10
YDR359C	0.625368	MSN4	YDR359C|EAF1|S000002767|Component of the NuA4 histone acetyltransferase complex; required for initiation of pre-meiotic DNA replication, probably due to its requirement for significant expression of IME1
YBR008C	0.622281	MSN4	YBR008C|FLR1|S000000212|Plasma membrane multidrug transporter of the major facilitator superfamily, involved in efflux of fluconazole, diazaborine, benomyl, methotrexate, and other drugs
YLL042C	0.620556	MSN4	YLL042C|ATG10|S000003965|E2-like conjugating enzyme that mediates formation of the Atg12p-Atg5p conjugate, which is a critical step in autophagy
YKL220C	0.61626	MSN4	YKL220C|FRE2|S000001703|Ferric reductase and cupric reductase, reduces siderophore-bound iron and oxidized copper prior to uptake by transporters; expression induced by low iron levels but not by low copper levels
YGR250C	0.616064	MSN4	YGR250C||S000003482|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YLR121C	0.614584	MSN4	YLR121C|YPS3|S000004111|Aspartic protease, attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor
YHR217C	0.609982	MSN4	YHR217C||S000001260|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; located in the telomeric region TEL08R.
YMR084W	0.609535	MSN4	YMR084W||S000004689|Putative protein of unknown function; YMR084W and adjacent ORF YMR085W are merged in related strains
YGR209C	0.605526	MSN4	YGR209C|TRX2|S000003441|Cytoplasmic thioredoxin isoenzyme of the thioredoxin system which protects cells against oxidative and reductive stress, forms LMA1 complex with Pbi2p, acts as a cofactor for Tsa1p, required for ER-Golgi transport and vacuole inheritance
YGL053W	0.601139	MSN4	YGL053W|PRM8|S000003021|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; member of DUP240 gene family
YGL180W	0.600822	MSN4	YGL180W|ATG1|S000003148|Protein serine/threonine kinase required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; during autophagy forms a complex with Atg13p and Atg17p
YNR002C	0.600145	MSN4	YNR002C|ATO2|S000005285|Putative transmembrane protein involved in export of ammonia, a starvation signal that promotes cell death in aging colonies; phosphorylated in mitochondria; member of the TC 9.B.33 YaaH family; homolog of Ady2p and Y. lipolytica Gpr1p
YBL100C	0.599778	MSN4	YBL100C||S000000196|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; almost completely overlaps the 5' end of ATP1
YNL282W	0.599132	MSN4	YNL282W|POP3|S000005226|Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursors to generate mature 5' ends
YCR079W	0.598553	MSN4	YCR079W|PTC6|S000002133|Mitochondrial protein phosphatase of type 2C with similarity to mammalian PP1Ks; involved in mitophagy; null mutant is sensitive to rapamycin and has decreased phosphorylation of the Pda1 subunit of pyruvate dehydrogenase
YPL166W	0.597891	MSN4	YPL166W|ATG29|S000006087|Protein specifically required for autophagy; may function in autophagosome formation at the pre-autophagosomal structure in collaboration with other autophagy proteins
YAR035W	0.59668	MSN4	YAR035W|YAT1|S000000080|Outer mitochondrial carnitine acetyltransferase, minor ethanol-inducible enzyme involved in transport of activated acyl groups from the cytoplasm into the mitochondrial matrix; phosphorylated
YPR154W	0.595804	MSN4	YPR154W|PIN3|S000006358|Protein that induces appearance of [PIN+] prion when overproduced
YBL029C-A	0.594398	MSN4	YBL029C-A||S000007591|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; has potential orthologs in Saccharomyces species and in Yarrowia lipolytica
YOR231W	0.594007	MSN4	YOR231W|MKK1|S000005757|Mitogen-activated kinase kinase involved in protein kinase C signaling pathway that controls cell integrity; upon activation by Bck1p phosphorylates downstream target, Slt2p; functionally redundant with Mkk2p
YHL032C	0.591593	MSN4	YHL032C|GUT1|S000001024|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
YKL028W	0.590868	MSN4	YKL028W|TFA1|S000001511|TFIIE large subunit, involved in recruitment of RNA polymerase II to the promoter, activation of TFIIH, and promoter opening
YCL033C	0.586947	MSN4	YCL033C||S000000538|Putative protein-methionine-R-oxide reductase; involved in response to oxidative stress; similar to mouse Sepx1p and fly SelRp; YCL033C is not an essential gene
YLL047W	0.58684	MSN4	YLL047W||S000003970|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene RNP1
YJL205C	0.58646	MSN4	YJL205C|NCE101|S000003742|Protein of unknown function, involved in secretion of proteins that lack classical secretory signal sequences
YGR066C	0.58601	MSN4	YGR066C||S000003298|Putative protein of unknown function
YBR056W	0.584575	MSN4	YBR056W||S000000260|Putative cytoplasmic protein of unknown function
YDL245C	0.583887	MSN4	YDL245C|HXT15|S000002404|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
YIL054W	0.583725	MSN4	YIL054W||S000001316|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR394W	0.582963	MSN4	YOR394W|PAU21|S000005921|Hypothetical protein
YDR397C	0.579128	MSN4	YDR397C|NCB2|S000002805|Subunit of a heterodimeric NC2 transcription regulator complex with Bur6p; complex binds to TBP and can repress transcription by preventing preinitiation complex assembly or stimulate activated transcription; homologous to human NC2beta
YLR267W	0.578973	MSN4	YLR267W|BOP2|S000004257|Protein of unknown function, overproduction suppresses a pam1 slv3 double null mutation
YJL082W	0.578367	MSN4	YJL082W|IML2|S000003618|Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR174W	0.576705	MSN4	YLR174W|IDP2|S000004164|Cytosolic NADP-specific isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate; levels are elevated during growth on non-fermentable carbon sources and reduced during growth on glucose
YML066C	0.575736	MSN4	YML066C|SMA2|S000004531|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YPR098C	0.575583	MSN4	YPR098C||S000006302|Protein of unknown function, localized to the mitochondrial outer membrane
YPL262W	0.573873	MSN4	YPL262W|FUM1|S000006183|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; phosphorylated in mitochondria
YNL037C	0.56818	MSN4	YNL037C|IDH1|S000004982|Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle
YBR295W	0.561761	MSN4	YBR295W|PCA1|S000000499|Cadmium transporting P-type ATPase; may also have a role in copper and iron homeostasis; S288C and most other lab strains contain a G970R mutation which eliminates normal cadmium transport function
YGL136C	0.560209	MSN4	YGL136C|MRM2|S000003104|Mitochondrial 2' O-ribose methyltransferase, required for methylation of U(2791) in 21S rRNA; MRM2 deletion confers thermosensitive respiration and loss of mitochondrial DNA; has similarity to Spb1p and Trm7p, and to E. coli FtsJ/RrmJ
YPL058C	0.557859	MSN4	YPL058C|PDR12|S000005979|Plasma membrane ATP-binding cassette (ABC) transporter, weak-acid-inducible multidrug transporter required for weak organic acid resistance; induced by sorbate and benzoate and regulated by War1p; mutants exhibit sorbate hypersensitivity
YLR437C-A	0.555683	MSN4	YLR437C-A||S000028684|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF CAR2/YLR438W
YDR233C	0.555198	MSN4	YDR233C|RTN1|S000002641|ER membrane protein that interacts with exocyst subunit Sec6p and with Yip3p; also interacts with Sbh1p; null mutant has an altered (mostly cisternal) ER morphology; member of the RTNLA (reticulon-like A) subfamily
YOL059W	0.553546	MSN4	YOL059W|GPD2|S000005420|NAD-dependent glycerol 3-phosphate dehydrogenase, homolog of Gpd1p, expression is controlled by an oxygen-independent signaling pathway required to regulate metabolism under anoxic conditions; located in cytosol and mitochondria
YDR380W	0.552375	MSN4	YDR380W|ARO10|S000002788|Phenylpyruvate decarboxylase, catalyzes decarboxylation of phenylpyruvate to phenylacetaldehyde, which is the first specific step in the Ehrlich pathway
YDR530C	0.546068	MSN4	YDR530C|APA2|S000002938|Diadenosine 5',5''-P1,P4-tetraphosphate phosphorylase II (AP4A phosphorylase), involved in catabolism of bis(5'-nucleosidyl) tetraphosphates; has similarity to Apa1p
YEL030W	0.545602	MSN4	YEL030W|ECM10|S000000756|Heat shock protein of the Hsp70 family, localized in mitochondrial nucleoids, plays a role in protein translocation, interacts with Mge1p in an ATP-dependent manner; overexpression induces extensive mitochondrial DNA aggregations
YMR243C	0.545471	MSN4	YMR243C|ZRC1|S000004856|Vacuolar membrane zinc transporter, transports zinc from the cytosol into the vacuole for storage; also has a role in resistance to zinc shock resulting from a sudden influx of zinc into the cytoplasm
YKR089C	0.54537	MSN4	YKR089C|TGL4|S000001797|Triacylglycerol lipase involved in triacylglycerol mobilization and degradation; found in lipid particles; potential Cdc28p substrate
YBR099C	0.545095	MSN4	YBR099C||S000000303|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified gene MMS4
YNL173C	0.543685	MSN4	YNL173C|MDG1|S000005117|Plasma membrane protein involved in G-protein mediated pheromone signaling pathway; overproduction suppresses bem1 mutations
YOL013C	0.539831	MSN4	YOL013C|HRD1|S000005373|Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger
YGL156W	0.538233	MSN4	YGL156W|AMS1|S000003124|Vacuolar alpha mannosidase, involved in free oligosaccharide (fOS) degradation; delivered to the vacuole in a novel pathway separate from the secretory pathway
YKR011C	0.52856	MSN4	YKR011C||S000001719|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus
YLR347C	0.526806	MSN4	YLR347C|KAP95|S000004339|Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex
YER010C	0.525558	MSN4	YER010C||S000000812|Protein of unknown function, forms a ring-shaped homotrimer; has similarity to members of the prokaryotic rraA family; possibly involved in a phosphotransfer reaction
YOL157C	0.521423	MSN4	YOL157C||S000005517|Putative protein of unknown function
YOR328W	0.519504	MSN4	YOR328W|PDR10|S000005855|ATP-binding cassette (ABC) transporter, multidrug transporter involved in the pleiotropic drug resistance network; regulated by Pdr1p and Pdr3p
YOR114W	0.517677	MSN4	YOR114W||S000005640|Putative protein of unknown function; null mutant is viable
YGL203C	0.517664	MSN4	YGL203C|KEX1|S000003171|Protease involved in the processing of killer toxin and alpha factor precursor; cleaves Lys and Arg residues from the C-terminus of peptides and proteins
YOR064C	0.516734	MSN4	YOR064C|YNG1|S000005590|Subunit of the NuA3 histone acetyltransferase complex that acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3, has similarity to the human tumor suppressor ING1
YDR079W	0.511201	MSN4	YDR079W|PET100|S000002486|Chaperone that specifically facilitates the assembly of cytochrome c oxidase, integral to the mitochondrial inner membrane; interacts with a subcomplex of subunits VII, VIIa, and VIII (Cox7p, Cox9p, and Cox8p) but not with the holoenzyme
YPL032C	0.506702	MSN4	YPL032C|SVL3|S000005953|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
YPR151C	0.505535	MSN4	YPR151C|SUE1|S000006355|Mitochondrial protein required for degradation of unstable forms of cytochrome c
YBL075C	0.504619	MSN4	YBL075C|SSA3|S000000171|ATPase involved in protein folding and the response to stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm
YGL163C	0.501679	MSN4	YGL163C|RAD54|S000003131|DNA-dependent ATPase, stimulates strand exchange by modifying the topology of double-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; member of the SWI/SNF family
YLR177W	0.501569	MSN4	YLR177W||S000004167|Putative protein of unknown function; phosphorylated by Dbf2p-Mob1p in vitro; some strains contain microsatellite polymophisms at this locus; YLR177W is not an essential gene
YMR031W-A	0.499483	MSN4	YMR031W-A||S000004634|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; null mutant displays shortened telomeres; partially overlaps the uncharacterized ORF YMR031C
YJL166W	0.498746	MSN4	YJL166W|QCR8|S000003702|Subunit 8 of ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; oriented facing the intermembrane space; expression is regulated by Abf1p and Cpf1p
YLR176C	0.496401	MSN4	YLR176C|RFX1|S000004166|Major transcriptional repressor of DNA-damage-regulated genes, recruits repressors Tup1p and Cyc8p to their promoters; involved in DNA damage and replication checkpoint pathway; similar to a family of mammalian DNA binding RFX1-4 proteins
YGR141W	0.496314	MSN4	YGR141W|VPS62|S000003373|Vacuolar protein sorting (VPS) protein required for cytoplasm to vacuole targeting of proteins
YFL021W	0.494228	MSN4	YFL021W|GAT1|S000001873|Transcriptional activator of genes involved in nitrogen catabolite repression; contains a GATA-1-type zinc finger DNA-binding motif; activity and localization regulated by nitrogen limitation and Ure2p
YML117W	0.492307	MSN4	YML117W|NAB6|S000004585|Putative RNA-binding protein, based on computational analysis of large-scale protein-protein interaction data
YBR262C	0.492074	MSN4	YBR262C|AIM5|S000000466|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss and reduced growth rate in minimal glycerol media
YMR145C	0.490234	MSN4	YMR145C|NDE1|S000004753|Mitochondrial external NADH dehydrogenase, a type II NAD(P)H:quinone oxidoreductase that catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p provide cytosolic NADH to the mitochondrial respiratory chain
YBR169C	0.48753	MSN4	YBR169C|SSE2|S000000373|Member of the heat shock protein 70 (HSP70) family; may be involved in protein folding; localized to the cytoplasm; highly homologous to the heat shock protein Sse1p
YBL086C	0.486554	MSN4	YBL086C||S000000182|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YDR504C	0.485132	MSN4	YDR504C|SPG3|S000002912|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YDR335W	0.483775	MSN4	YDR335W|MSN5|S000002743|Karyopherin involved in nuclear import and export; shown to be responsible for nuclear import of replication protein A and for export of several proteins including Swi6p, Far1p, and Pho4p; cargo dissociation involves binding to RanGTP
YDR282C	0.483128	MSN4	YDR282C||S000002690|Putative protein of unknown function
YAR027W	0.483119	MSN4	YAR027W|UIP3|S000000075|Putative integral membrane protein of unknown function; interacts with Ulp1p at the nuclear periphery; member of DUP240 gene family
YMR122C	0.480289	MSN4	YMR122C||S000004729|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNR007C	0.47919	MSN4	YNR007C|ATG3|S000005290|E2-like enzyme involved in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; plays a role in formation of Atg8p-phosphatidylethanolamine conjugates, which are involved in membrane dynamics during autophagy and Cvt
YDL195W	0.47812	MSN4	YDL195W|SEC31|S000002354|Essential phosphoprotein component (p150) of the COPII coat of secretory pathway vesicles, in complex with Sec13p; required for ER-derived transport vesicle formation
YER098W	0.477089	MSN4	YER098W|UBP9|S000000900|Ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YGL071W	0.476517	MSN4	YGL071W|AFT1|S000003039|Transcription factor involved in iron utilization and homeostasis; binds the consensus site PyPuCACCCPu and activates the expression of target genes in response to changes in iron availability
YHR145C	0.475627	MSN4	YHR145C||S000001188|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR269W	0.472296	MSN4	YGR269W||S000003501|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF HUA1/YGR268C
YHR150W	0.471518	MSN4	YHR150W|PEX28|S000001193|Peroxisomal integral membrane peroxin, involved in the regulation of peroxisomal size, number and distribution; genetic interactions suggest that Pex28p and Pex29p act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p
YLR337C	0.470324	MSN4	YLR337C|VRP1|S000004329|Proline-rich actin-associated protein involved in cytoskeletal organization and cytokinesis; related to mammalian Wiskott-Aldrich syndrome protein (WASP)-interacting protein (WIP)
YMR278W	0.46991	MSN4	YMR278W|PGM3|S000004891|Phosphoglucomutase, catalyzes interconversion of glucose-1-phosphate and glucose-6-phospate; transcription induced in response to stress; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; non-essential
YKL016C	0.46899	MSN4	YKL016C|ATP7|S000001499|Subunit d of the stator stalk of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YPL282C	0.468441	MSN4	YPL282C|PAU22|S000006203|Hypothetical protein
YIL134C-A	0.468303	MSN4	YIL134C-A||S000028556|Putative protein of unknown function, identified by fungal homology and RT-PCR
YHR198C	0.465376	MSN4	YHR198C|AIM18|S000001241|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YPL018W	0.464995	MSN4	YPL018W|CTF19|S000005939|Outer kinetochore protein, required for accurate mitotic chromosome segregation; component of the kinetochore sub-complex COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) that functions as a platform for kinetochore assembly
YGR230W	0.46364	MSN4	YGR230W|BNS1|S000003462|Protein with some similarity to Spo12p; overexpression bypasses need for Spo12p, but not required for meiosis
YGR072W	0.463561	MSN4	YGR072W|UPF3|S000003304|Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
YHR095W	0.461685	MSN4	YHR095W||S000001137|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL146W	0.461216	MSN4	YNL146W||S000005090|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YNL146W is not an essential gene
YNL005C	0.460692	MSN4	YNL005C|MRP7|S000004950|Mitochondrial ribosomal protein of the large subunit
YLR189C	0.458389	MSN4	YLR189C|ATG26|S000004179|UDP-glucose:sterol glucosyltransferase, conserved enzyme involved in synthesis of sterol glucoside membrane lipids; in contrast to ATG26 from P. pastoris, S. cerevisiae ATG26 is not involved in autophagy
YDR374C	0.458372	MSN4	YDR374C||S000002782|Putative protein of unknown function
YNR032C-A	0.457421	MSN4	YNR032C-A|HUB1|S000007251|Ubiquitin-like protein modifier, may function in modification of Sph1p and Hbt1p, functionally complemented by the human or S. pombe ortholog; mechanism of Hub1p adduct formation not yet clear
YEL024W	0.455174	MSN4	YEL024W|RIP1|S000000750|Ubiquinol-cytochrome-c reductase, a Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex; transfers electrons from ubiquinol to cytochrome c1 during respiration
YCR086W	0.452805	MSN4	YCR086W|CSM1|S000000682|Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance
YEL073C	0.451017	MSN4	YEL073C||S000000799|Putative protein of unknown function; located adjacent to ARS503 and the telomere on the left arm of chromosome V; regulated by inositol/choline
YOL126C	0.448074	MSN4	YOL126C|MDH2|S000005486|Cytoplasmic malate dehydrogenase, one of three isozymes that catalyze interconversion of malate and oxaloacetate; involved in the glyoxylate cycle and gluconeogenesis during growth on two-carbon compounds; interacts with Pck1p and Fbp1
YOR388C	0.446869	MSN4	YOR388C|FDH1|S000005915|NAD(+)-dependent formate dehydrogenase, may protect cells from exogenous formate
YKL070W	0.446315	MSN4	YKL070W||S000001553|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPL274W	0.445988	MSN4	YPL274W|SAM3|S000006195|High-affinity S-adenosylmethionine permease, required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p
YLR113W	0.444514	MSN4	YLR113W|HOG1|S000004103|Mitogen-activated protein kinase involved in osmoregulation via three independent osmosensors; mediates the recruitment and activation of RNA Pol II at Hot1p-dependent promoters; localization regulated by Ptp2p and Ptp3p
YPR030W	0.442107	MSN4	YPR030W|CSR2|S000006234|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
YER133W-A	0.440316	MSN4	YER133W-A||S000028756|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized gene YER134C.
YDR204W	0.439528	MSN4	YDR204W|COQ4|S000002612|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; component of a mitochondrial ubiquinone-synthesizing complex
YDR501W	0.437551	MSN4	YDR501W|PLM2|S000002909|Protein required for partitioning of the 2-micron plasmid
YOL160W	0.435141	MSN4	YOL160W||S000005520|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL243W	0.431586	MSN4	YNL243W|SLA2|S000005187|Transmembrane actin-binding protein involved in membrane cytoskeleton assembly and cell polarization; adaptor protein that links actin to clathrin and endocytosis; present in the actin cortical patch of the emerging bud tip; dimer in vivo
YOR389W	0.430911	MSN4	YOR389W||S000005916|Putative protein of unknown function; expression regulated by copper levels
YEL074W	0.42707	MSN4	YEL074W||S000000800|Hypothetical protein
YJR159W	0.425258	MSN4	YJR159W|SOR1|S000003920|Sorbitol dehydrogenase; expression is induced in the presence of sorbitol
YLL029W	0.425144	MSN4	YLL029W|FRA1|S000003952|Protein involved in negative regulation of transcription of iron regulon; forms an iron independent complex with Fra2p, Grx3p, and Grx4p; cytosolic; mutant fails to repress transcription of iron regulon and is defective in spore formation
YFR010W-A	0.422841	MSN4	YFR010W-A||S000028824|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the uncharacterized gene YFR011C; identified by expression profiling and mass spectrometry
YMR158W-B	0.422544	MSN4	YMR158W-B||S000004768|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene ATG16/YMR159C
YBR204C	0.421565	MSN4	YBR204C||S000000408|Serine hydrolase; YBR204C is not an essential gene
YJL186W	0.42086	MSN4	YJL186W|MNN5|S000003722|Alpha-1,2-mannosyltransferase, responsible for addition of the second alpha-1,2-linked mannose of the branches on the mannan backbone of oligosaccharides, localizes to an early Golgi compartment
YBR208C	0.420859	MSN4	YBR208C|DUR1,2|S000000412|Urea amidolyase, contains both urea carboxylase and allophanate hydrolase activities, degrades urea to CO2 and NH3; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YHL037C	0.420152	MSN4	YHL037C||S000001029|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL082C	0.415106	MSN4	YPL082C|MOT1|S000006003|Essential abundant protein involved in regulation of transcription, removes Spt15p (TBP) from DNA via its C-terminal ATPase activity, forms a complex with TBP that binds TATA DNA with high affinity but with altered specificity
YDL070W	0.40903	MSN4	YDL070W|BDF2|S000002228|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
YEL059C-A	0.408035	MSN4	YEL059C-A|SOM1|S000002954|Subunit of the mitochondrial inner membrane peptidase, which is required for maturation of mitochondrial proteins of the intermembrane space; Som1p facilitates cleavage of a subset of substrates
YHR202W	0.407175	MSN4	YHR202W||S000001245|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole, while HA-tagged protein is found in the soluble fraction, suggesting cytoplasmic localization
YKL162C	0.407144	MSN4	YKL162C||S000001645|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the mitochondrion
YGL063W	0.407096	MSN4	YGL063W|PUS2|S000003031|Mitochondrial tRNA:pseudouridine synthase; acts at positions 27 and 28, but not at position 72; efficiently and rapidly targeted to mitochondria, specifically dedicated to mitochondrial tRNA modification
YDL109C	0.407077	MSN4	YDL109C||S000002267|Putative lipase; involved in lipid metabolism; YDL109C is not an essential gene
YLR439W	0.405663	MSN4	YLR439W|MRPL4|S000004431|Mitochondrial ribosomal protein of the large subunit
YDR307W	0.398755	MSN4	YDR307W||S000002715|Putative protein of unknown function
YHR218W	0.397686	MSN4	YHR218W||S000001261|Helicase-like protein encoded within the telomeric Y' element
YHL035C	0.397374	MSN4	YHL035C|VMR1|S000001027|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; member of the ATP-binding cassette (ABC) family; potential Cdc28p substrate; detected in purified mitochondria in high-throughput studies
YEL071W	0.396089	MSN4	YEL071W|DLD3|S000000797|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
YBR060C	0.3955	MSN4	YBR060C|ORC2|S000000264|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; phosphorylated by Cdc28p
YDR085C	0.393663	MSN4	YDR085C|AFR1|S000002492|Alpha-factor pheromone receptor regulator, negatively regulates pheromone receptor signaling; required for normal mating projection (shmoo) formation; required for Spa2p to recruit Mpk1p to shmoo tip during mating; interacts with Cdc12p
YGL162W	0.392613	MSN4	YGL162W|SUT1|S000003130|Transcription factor of the Zn[II]2Cys6 family involved in sterol uptake; involved in induction of hypoxic gene expression
YNL339C	0.39102	MSN4	YNL339C|YRF1-6|S000005283|Helicase encoded by the Y' element of subtelomeric regions, highly expressed in the mutants lacking the telomerase component TLC1; potentially phosphorylated by Cdc28p
YJR044C	0.390518	MSN4	YJR044C|VPS55|S000003805|Late endosomal protein involved in late endosome to vacuole trafficking; functional homolog of human obesity receptor gene-related protein (OB-RGRP)
YAR019C	0.386608	MSN4	YAR019C|CDC15|S000000072|Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p
YNR071C	0.385188	MSN4	YNR071C||S000005354|Putative protein of unknown function
YFL063W	0.384896	MSN4	YFL063W||S000001831|Dubious open reading frame, based on available experimental and comparative sequence data
YGL064C	0.383924	MSN4	YGL064C|MRH4|S000003032|Mitochondrial ATP-dependent RNA helicase of the DEAD-box family, plays an essential role in mitochondrial function
YMR124W	0.383247	MSN4	YMR124W||S000004731|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; interacts with Crm1p in two-hybrid assay; YMR124W is not an essential gene
YMR089C	0.381529	MSN4	YMR089C|YTA12|S000004695|Component, with Afg3p, of the mitochondrial inner membrane m-AAA protease that mediates degradation of misfolded or unassembled proteins and is also required for correct assembly of mitochondrial enzyme complexes
YML003W	0.381153	MSN4	YML003W||S000004462|Putative protein of unknown function
YOL051W	0.377664	MSN4	YOL051W|GAL11|S000005411|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; affects transcription by acting as target of activators and repressors
YAR019W-A	0.376557	MSN4	YAR019W-A||S000028735|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPR024W	0.376166	MSN4	YPR024W|YME1|S000006228|Subunit, with Mgr1p, of the mitochondrial inner membrane i-AAA protease complex, which is responsible for degradation of unfolded or misfolded mitochondrial gene products; mutation causes an elevated rate of mitochondrial turnover
YPL027W	0.37518	MSN4	YPL027W|SMA1|S000005948|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YNR063W	0.37362	MSN4	YNR063W||S000005346|Putative zinc-cluster protein of unknown function
YIR028W	0.371202	MSN4	YIR028W|DAL4|S000001467|Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YGL160W	0.371057	MSN4	YGL160W|AIM14|S000003128|Putative protein of unknown function; similar to iron/copper reductases (FRE1-8), possibly involved in iron homeostasis; may interact with ribosomes, null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YKL094W	0.370488	MSN4	YKL094W|YJU3|S000001577|Serine hydrolase with sequence similarity to monoglyceride lipase (MGL), localizes to lipid particles
YDL185W	0.367343	MSN4	YDL185W|TFP1|S000002344|Vacuolar ATPase V1 domain subunit A containing the catalytic nucleotide binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease
YDR435C	0.366449	MSN4	YDR435C|PPM1|S000002843|Carboxyl methyltransferase, methylates the C terminus of the protein phosphatase 2A catalytic subunit (Pph21p or Pph22p), which is important for complex formation with regulatory subunits
YIL006W	0.366044	MSN4	YIL006W|YIA6|S000001268|Mitochondrial NAD+ transporter, involved in the transport of NAD+ into the mitochondria (see also YEA6); member of the mitochondrial carrier subfamily; disputed role as a pyruvate transporter; has putative mouse and human orthologs
YJR119C	0.365952	MSN4	YJR119C|JHD2|S000003880|JmjC domain family histone demethylase specific for H3-K4 (lysine at position 4 of the histone H3 protein); removes methyl groups specifically added by Set1p methyltransferase
YMR140W	0.364886	MSN4	YMR140W|SIP5|S000004748|Protein of unknown function; interacts with both the Reg1p/Glc7p phosphatase and the Snf1p kinase
YDR242W	0.360109	MSN4	YDR242W|AMD2|S000002650|Putative amidase
YDR438W	0.358205	MSN4	YDR438W|THI74|S000002846|Mitochondrial transporter repressible by thiamine
YFL064C	0.35745	MSN4	YFL064C||S000001830|Putative protein of unknown function
YOR035C	0.356786	MSN4	YOR035C|SHE4|S000005561|Protein containing a UCS (UNC-45/CRO1/SHE4) domain, binds to myosin motor domains to regulate myosin function; involved in endocytosis, polarization of the actin cytoskeleton, and asymmetric mRNA localization
YOR292C	0.356465	MSN4	YOR292C||S000005818|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YOR292C is not an essential gene
YLR436C	0.355451	MSN4	YLR436C|ECM30|S000004428|Non-essential protein of unknown function
YBL045C	0.355296	MSN4	YBL045C|COR1|S000000141|Core subunit of the ubiquinol-cytochrome c reductase complex (bc1 complex), which is a component of the mitochondrial inner membrane electron transport chain
YEL075C	0.355064	MSN4	YEL075C||S000000801|Putative protein of unknown function
YGR222W	0.35367	MSN4	YGR222W|PET54|S000003454|Mitochondrial inner membrane protein that binds to the 5' UTR of the COX3 mRNA to activate its translation together with Pet122p and Pet494p; also binds to the COX1 Group I intron AI5 beta to facilitate exon ligation during splicing
YPR117W	0.352368	MSN4	YPR117W||S000006321|Putative protein of unknown function
YFL062W	0.350769	MSN4	YFL062W|COS4|S000001832|Protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YBR033W	0.349623	MSN4	YBR033W|EDS1|S000000237|Putative zinc cluster protein; YBR033W is not an essential gene
YDR313C	0.347148	MSN4	YDR313C|PIB1|S000002721|RING-type ubiquitin ligase of the endosomal and vacuolar membranes, binds phosphatidylinositol(3)-phosphate; contains a FYVE finger domain
YDR455C	0.347131	MSN4	YDR455C||S000002863|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDR456W
YOR329W-A	0.346952	MSN4	YOR329W-A||S000028585|Dubious open reading frame, unlikely to encode a functional protein; identified by fungal homology and RT-PCR
YOL071W	0.346624	MSN4	YOL071W|EMI5|S000005432|Non-essential protein of unknown function required for transcriptional induction of the early meiotic-specific transcription factor IME1, also required for sporulation
YDR275W	0.344377	MSN4	YDR275W|BSC2|S000002683|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YDR456W	0.34317	MSN4	YDR456W|NHX1|S000002864|Endosomal Na+/H+ exchanger, required for intracellular sequestration of Na+; required for osmotolerance to acute hypertonic shock
YMR014W	0.342929	MSN4	YMR014W|BUD22|S000004616|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YDR444W	0.342688	MSN4	YDR444W||S000002852|Putative protein of unknown function
YOL100W	0.342451	MSN4	YOL100W|PKH2|S000005460|Serine/threonine protein kinase involved in sphingolipid-mediated signaling pathway that controls endocytosis; activates Ypk1p and Ykr2p, components of signaling cascade required for maintenance of cell wall integrity; redundant with Pkh1p
YHR042W	0.339988	MSN4	YHR042W|NCP1|S000001084|NADP-cytochrome P450 reductase; involved in ergosterol biosynthesis; associated and coordinately regulated with Erg11p
YOR194C	0.33953	MSN4	YOR194C|TOA1|S000005720|TFIIA large subunit; involved in transcriptional activation, acts as antirepressor or as coactivator; homologous to largest and second largest subunits of human and Drosophila TFIIA
YDR009W	0.338121	MSN4	YDR009W|GAL3|S000002416|Transcriptional regulator involved in activation of the GAL genes in response to galactose; forms a complex with Gal80p to relieve Gal80p inhibition of Gal4p; binds galactose and ATP but does not have galactokinase activity
YDR293C	0.337964	MSN4	YDR293C|SSD1|S000002701|Protein with a role in maintenance of cellular integrity, interacts with components of the TOR pathway; ssd1 mutant of a clinical S. cerevisiae strain displays elevated virulence
YPR085C	0.335306	MSN4	YPR085C||S000006289|Putative protein of unknown function; YPR085C is an essential gene
YBL042C	0.335007	MSN4	YBL042C|FUI1|S000000138|High affinity uridine permease, localized to the plasma membrane; not involved in uracil transport
YCR048W	0.330348	MSN4	YCR048W|ARE1|S000000644|Acyl-CoA:sterol acyltransferase, isozyme of Are2p; endoplasmic reticulum enzyme that contributes the major sterol esterification activity in the absence of oxygen
YAL020C	0.329296	MSN4	YAL020C|ATS1|S000000018|Protein required, with Elongator complex, Kti11p, and Kti12p, for modification of wobble nucleosides in tRNA; has a potential role in regulatory interactions between microtubules and the cell cycle
YEL069C	0.327636	MSN4	YEL069C|HXT13|S000000795|Hexose transporter, induced in the presence of non-fermentable carbon sources, induced by low levels of glucose, repressed by high levels of glucose
YDL227C	0.326832	MSN4	YDL227C|HO|S000002386|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
YMR264W	0.32614	MSN4	YMR264W|CUE1|S000004877|Endoplasmic reticulum membrane protein that recruits the ubiquitin-conjugating enzyme Ubc7p to the ER where it functions in protein degradation; contains a CUE domain that binds ubiquitin to facilitate intramolecular monoubiquitination
YCR085W	0.325991	MSN4	YCR085W||S000000681|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDL026W	0.325027	MSN4	YDL026W||S000002184|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YIR016W	0.323627	MSN4	YIR016W||S000001455|Putative protein of unknown function; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR016W is a non-essential gene
YFL042C	0.320347	MSN4	YFL042C||S000001852|Putative protein of unknown function; YFL042C is not an essential gene
YMR261C	0.32015	MSN4	YMR261C|TPS3|S000004874|Regulatory subunit of trehalose-6-phosphate synthase/phosphatase complex, which synthesizes the storage carbohydrate trehalose; expression is induced by stress conditions and repressed by the Ras-cAMP pathway
YER079W	0.317777	MSN4	YER079W||S000000881|Putative protein of unknown function
YOR317W	0.317132	MSN4	YOR317W|FAA1|S000005844|Long chain fatty acyl-CoA synthetase with a preference for C12:0-C16:0 fatty acids; involved in the activation of imported fatty acids; localized to both lipid particles and mitochondrial outer membrane; essential for stationary phase
YIR002C	0.314724	MSN4	YIR002C|MPH1|S000001441|Member of the DEAH family of helicases, functions in an error-free DNA damage bypass pathway that involves homologous recombination, mutations confer a mutator phenotype
YDR078C	0.313599	MSN4	YDR078C|SHU2|S000002485|Protein of unassigned function involved in mutation suppression, important for error-free repair of spontaneous and induced DNA lesions to protect the genome from mutation; associates with Shu1p, Psy3p, and Csm2p
YCR069W	0.313377	MSN4	YCR069W|CPR4|S000000665|Peptidyl-prolyl cis-trans isomerase (cyclophilin), catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; has a potential role in the secretory pathway
YPL056C	0.313256	MSN4	YPL056C||S000005977|Putative protein of unknown function; deletion mutant is fluconazole resistant
YDL246C	0.312473	MSN4	YDL246C|SOR2|S000002405|Protein of unknown function, computational analysis of large-scale protein-protein interaction data suggests a possible role in fructose or mannose metabolism
YDR239C	0.312261	MSN4	YDR239C||S000002647|Protein of unknown function that may interact with ribosomes, based on co-purification experiments
YLR207W	0.311136	MSN4	YLR207W|HRD3|S000004197|Resident protein of the ER membrane that plays a central role in ER-associated protein degradation (ERAD), forms HRD complex with Hrd1p and ERAD determinants that engages in lumen to cytosol communication and coordination of ERAD events
YBR053C	0.310647	MSN4	YBR053C||S000000257|Putative protein of unknown function; induced by cell wall perturbation
YGL117W	0.309865	MSN4	YGL117W||S000003085|Putative protein of unknown function
YJR154W	0.307105	MSN4	YJR154W||S000003915|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YGR153W	0.304967	MSN4	YGR153W||S000003385|Putative protein of unknown function
YGR011W	0.304347	MSN4	YGR011W||S000003243|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR070C	0.300737	MSN4	YLR070C|XYL2|S000004060|Xylitol dehydrogenase, converts xylitol to D-xylulose in the endogenous xylose utilization pathway
YMR193W	0.30073	MSN4	YMR193W|MRPL24|S000004806|Mitochondrial ribosomal protein of the large subunit
YAL067C	0.300108	MSN4	YAL067C|SEO1|S000000062|Putative permease, member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide
YLR454W	0.299172	MSN4	YLR454W|FMP27|S000004446|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER188C-A	0.297103	MSN4	YER188C-A||S000028764|Putative protein of unknown function
YIR017C	0.296905	MSN4	YIR017C|MET28|S000001456|Transcriptional activator in the Cbf1p-Met4p-Met28p complex, participates in the regulation of sulfur metabolism
YJL059W	0.295289	MSN4	YJL059W|YHC3|S000003595|Vacuolar membrane protein involved in the ATP-dependent transport of arginine into the vacuole and possibly in balancing ion homeostasis; homolog of human CLN3 involved in Batten disease (juvenile onset neuronal ceroid lipofuscinosis)
YOL159C-A	0.294319	MSN4	YOL159C-A||S000007627|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YCR105W	0.294213	MSN4	YCR105W|ADH7|S000000702|NADPH-dependent medium chain alcohol dehydrogenase with broad substrate specificity; member of the cinnamyl family of alcohol dehydrogenases; may be involved in fusel alcohol synthesis or in aldehyde tolerance
YAL067W-A	0.293205	MSN4	YAL067W-A||S000028593|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YAL019W-A	0.291775	MSN4	YAL019W-A||S000028729|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR270C	0.289336	MSN4	YBR270C|BIT2|S000000474|Hypothetical protein
YPL219W	0.289127	MSN4	YPL219W|PCL8|S000006140|Cyclin, interacts with Pho85p cyclin-dependent kinase (Cdk) to phosphorylate and regulate glycogen synthase, also activates Pho85p for Glc8p phosphorylation
YIR003W	0.288438	MSN4	YIR003W|AIM21|S000001442|Protein of unknown function; may interact with ribosomes; GFP-fusion protein colocalizes with Sac1p to the actin cytoskeleton; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YER189W	0.287723	MSN4	YER189W||S000000991|Putative protein of unknown function
YDL231C	0.287703	MSN4	YDL231C|BRE4|S000002390|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
YML035C	0.287545	MSN4	YML035C|AMD1|S000004498|AMP deaminase, tetrameric enzyme that catalyzes the deamination of AMP to form IMP and ammonia; may be involved in regulation of intracellular adenine nucleotide pools
YJL100W	0.286675	MSN4	YJL100W|LSB6|S000003636|Type II phosphatidylinositol 4-kinase that binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization
YGR203W	0.286563	MSN4	YGR203W||S000003435|Putative protein with sequence similarity to protein tyrosine phosphatases of the CDC25-like phosphatase family; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YKL192C	0.285466	MSN4	YKL192C|ACP1|S000001675|Mitochondrial matrix acyl carrier protein, involved in biosynthesis of octanoate, which is a precursor to lipoic acid; activated by phosphopantetheinylation catalyzed by Ppt2p
YCL057C-A	0.285182	MSN4	YCL057C-A||S000007547|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGR213C	0.284465	MSN4	YGR213C|RTA1|S000003445|Protein involved in 7-aminocholesterol resistance; has seven potential membrane-spanning regions; expression is induced under both low-heme and low-oxygen conditions
YKL037W	0.283963	MSN4	YKL037W|AIM26|S000001520|Putative protein of unknown function; null mutant is viable and displays increased frequency of mitochondrial genome loss (petite formation)
YCR018C-A	0.282369	MSN4	YCR018C-A||S000007230|Putative protein of unknown function; encoded opposite a Ty1 LTR
YMR053C	0.278436	MSN4	YMR053C|STB2|S000004657|Protein that interacts with Sin3p in a two-hybrid assay and is part of a large protein complex with Sin3p and Stb1p
YDL027C	0.277924	MSN4	YDL027C||S000002185|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDL027C is not an essential gene
YGL256W	0.277875	MSN4	YGL256W|ADH4|S000003225|Alcohol dehydrogenase isoenzyme type IV, dimeric enzyme demonstrated to be zinc-dependent despite sequence similarity to iron-activated alcohol dehydrogenases; transcription is induced in response to zinc deficiency
YDL230W	0.277467	MSN4	YDL230W|PTP1|S000002389|Phosphotyrosine-specific protein phosphatase that dephosphorylates a broad range of substrates in vivo, including Fpr3p; localized to the cytoplasm and the mitochondria
YDR402C	0.275765	MSN4	YDR402C|DIT2|S000002810|N-formyltyrosine oxidase, sporulation-specific microsomal enzyme involved in the production of N,N-bisformyl dityrosine required for spore wall maturation, homologous to cytochrome P-450s
YKL029C	0.27511	MSN4	YKL029C|MAE1|S000001512|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
YOL063C	0.273455	MSN4	YOL063C|CRT10|S000005424|Protein involved in transcriptional regulation of RNR2 and RNR3; expression of the gene is induced by DNA damage and null mutations confer increased resistance to hydroxyurea; N-terminal region has a leucine repeat and a WD40 repeat
YGL010W	0.271272	MSN4	YGL010W||S000002978|Putative protein of unknown function; YGL010W is not an essential gene
YOR057W	0.270145	MSN4	YOR057W|SGT1|S000005583|Probable cochaperone, regulates activity of Cyr1p (adenylyl cyclase); involved in assembly of the kinetochore complex, associates with the SCF (Skp1p/Cdc53p/F box protein) ubiquitin ligase complex
YDR248C	0.269887	MSN4	YDR248C||S000002656|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YCR061W	0.26955	MSN4	YCR061W||S000000657|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; induced by treatment with 8-methoxypsoralen and UVA irradiation
YDL160C	0.269365	MSN4	YDL160C|DHH1|S000002319|Cytoplasmic DExD/H-box helicase, stimulates mRNA decapping, coordinates distinct steps in mRNA function and decay, interacts with both the decapping and deadenylase complexes, may have a role in mRNA export and translation
YPL184C	0.267893	MSN4	YPL184C|MRN1|S000006105|Putative RNA binding protein
YJL036W	0.264782	MSN4	YJL036W|SNX4|S000003573|Sorting nexin, involved in the retrieval of late-Golgi SNAREs from the post-Golgi endosome to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX domain; forms complexes with Snx41p and with Atg20p
YGL250W	0.263673	MSN4	YGL250W|RMR1|S000003219|Protein required for meiotic recombination and gene conversion; null mutant displays reduced PIS1 expression and growth defects on non-fermentable carbon sources and minimal media; GFP-fusion protein localizes to both cytoplasm and nucleus
YIL143C	0.262745	MSN4	YIL143C|SSL2|S000001405|Component of the holoenzyme form of RNA polymerase transcription factor TFIIH, has DNA-dependent ATPase/helicase activity and is required, with Rad3p, for unwinding promoter DNA; involved in DNA repair; homolog of human ERCC3
YIL037C	0.260286	MSN4	YIL037C|PRM2|S000001299|Pheromone-regulated protein, predicted to have 4 transmembrane segments and a coiled coil domain; regulated by Ste12p
YDL115C	0.259587	MSN4	YDL115C|IWR1|S000002273|Protein of unknown function, deletion causes hypersensitivity to the K1 killer toxin
YOL111C	0.25958	MSN4	YOL111C|MDY2|S000005471|Protein required for efficient mating; involved in shmoo formation and nuclear migration in the pre-zygote; associates with ribosomes and interacts with YOR164C; contains a ubiquitin-like (UBL) domain
YEL017W	0.258573	MSN4	YEL017W|GTT3|S000000743|Protein of unknown function with a possible role in glutathione metabolism, as suggested by computational analysis of large-scale protein-protein interaction data; GFP-fusion protein localizes to the nuclear periphery
YKL100C	0.257212	MSN4	YKL100C||S000001583|Putative protein of unknown function with similarity to a human minor histocompatibility antigen; YKL100C is not an essential gene
YDL139C	0.257071	MSN4	YDL139C|SCM3|S000002298|Nonhistone component of centromeric chromatin that binds stoichiometrically to CenH3-H4 histones, required for kinetochore assembly; contains nuclear export signal (NES); required for G2/M progression and localization of Cse4p
YNL331C	0.256865	MSN4	YNL331C|AAD14|S000005275|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YPL123C	0.255799	MSN4	YPL123C|RNY1|S000006044|RNAse; member of the T(2) family of endoribonucleases
YBR035C	0.254705	MSN4	YBR035C|PDX3|S000000239|Pyridoxine (pyridoxamine) phosphate oxidase, has homologs in E. coli and Myxococcus xanthus; transcription is under the general control of nitrogen metabolism
YDL024C	0.252495	MSN4	YDL024C|DIA3|S000002182|Protein of unknown function, involved in invasive and pseudohyphal growth
YNL133C	0.252374	MSN4	YNL133C|FYV6|S000005077|Protein of unknown function, required for survival upon exposure to K1 killer toxin; proposed to regulate double-strand break repair via non-homologous end-joining
YCR024C-B	0.252358	MSN4	YCR024C-B||S000028818|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YOL156W	0.251002	MSN4	YOL156W|HXT11|S000005516|Putative hexose transporter that is nearly identical to Hxt9p, has similarity to major facilitator superfamily (MFS) transporters and is involved in pleiotropic drug resistance
YIL058W	0.24898	MSN4	YIL058W||S000001320|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR329C	0.246049	MSN4	YOR329C|SCD5|S000005856|Protein required for normal cortical actin organization and endocytosis; multicopy suppressor of clathrin deficiency; acts as a targeting subunit for protein phosphatase type 1
YLR211C	0.245415	MSN4	YLR211C||S000004201|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YLR211C is not an essential gene; ORF contains an intron
YGL176C	0.24526	MSN4	YGL176C||S000003144|Putative protein of unknown function; deletion mutant is viable and has no detectable phenotype
YLR131C	0.245119	MSN4	YLR131C|ACE2|S000004121|Transcription factor that activates expression of early G1-specific genes, localizes to daughter cell nuclei after cytokinesis and delays G1 progression in daughters, localization is regulated by phosphorylation; potential Cdc28p substrate
YBR001C	0.2426	MSN4	YBR001C|NTH2|S000000205|Putative neutral trehalase, required for thermotolerance and may mediate resistance to other cellular stresses
YGL124C	0.241547	MSN4	YGL124C|MON1|S000003092|Protein required for fusion of cvt-vesicles and autophagosomes with the vacuole; associates, as a complex with Ccz1p, with a perivacuolar compartment; potential Cdc28p substrate
YOR036W	0.240585	MSN4	YOR036W|PEP12|S000005562|Target membrane receptor (t-SNARE) for vesicular intermediates traveling between the Golgi apparatus and the vacuole; controls entry of biosynthetic, endocytic, and retrograde traffic into the prevacuolar compartment; syntaxin
YML058W	0.239493	MSN4	YML058W|SML1|S000004523|Ribonucleotide reductase inhibitor involved in regulating dNTP production; regulated by Mec1p and Rad53p during DNA damage and S phase
YER017C	0.237374	MSN4	YER017C|AFG3|S000000819|Component, with Yta12p, of the mitochondrial inner membrane m-AAA protease that mediates degradation of misfolded or unassembled proteins and is also required for correct assembly of mitochondrial enzyme complexes
YKL039W	0.234175	MSN4	YKL039W|PTM1|S000001522|Protein of unknown function, copurifies with late Golgi vesicles containing the v-SNARE Tlg2p
YHR077C	0.2341	MSN4	YHR077C|NMD2|S000001119|Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance
YER020W	0.232038	MSN4	YER020W|GPA2|S000000822|Nucleotide binding alpha subunit of the heterotrimeric G protein that interacts with the receptor Gpr1p, has signaling role in response to nutrients; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YPR155C	0.23203	MSN4	YPR155C|NCA2|S000006359|Protein involved in regulation of mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p) of the Fo-F1 ATP synthase; functions with Nca3p
YOR257W	0.22983	MSN4	YOR257W|CDC31|S000005783|Calcium-binding component of the spindle pole body (SPB) half-bridge, required for SPB duplication in mitosis and meiosis II; homolog of mammalian centrin; binds multiubiquitinated proteins and is involved in proteasomal protein degradation
YLR422W	0.228743	MSN4	YLR422W||S000004414|Protein of unknown function with similarity to human DOCK proteins (guanine nucleotide exchange factors); interacts with Ino4p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm, YLR422W is not an essential protein
YOR344C	0.225914	MSN4	YOR344C|TYE7|S000005871|Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif; binds E-boxes of glycolytic genes and contributes to their activation; may function as a transcriptional activator in Ty1-mediated gene expression
YDL234C	0.225025	MSN4	YDL234C|GYP7|S000002393|GTPase-activating protein for yeast Rab family members including: Ypt7p (most effective), Ypt1p, Ypt31p, and Ypt32p (in vitro); involved in vesicle mediated protein trafficking
YMR156C	0.224886	MSN4	YMR156C|TPP1|S000004765|DNA 3'-phosphatase that functions in repair of endogenous damage of double-stranded DNA, activity is specific for removal of 3' phosphates at strand breaks; has similarity to the l-2-haloacid dehalogenase superfamily
YHR074W	0.222883	MSN4	YHR074W|QNS1|S000001116|Glutamine-dependent NAD(+) synthetase, essential for the formation of NAD(+) from nicotinic acid adenine dinucleotide
YBR278W	0.221945	MSN4	YBR278W|DPB3|S000000482|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
YMR087W	0.219959	MSN4	YMR087W||S000004693|Putative ADP-ribose-1''-monophosphatase that converts ADP-ribose-1''-monophosphate to ADP-ribose; may have a role in tRNA splicing; contains an A1pp domain
YPL264C	0.218935	MSN4	YPL264C||S000006185|Putative membrane protein of unknown function; physically interacts with Hsp82p; YPL264C is not an essential gene
YLR203C	0.218228	MSN4	YLR203C|MSS51|S000004193|Nuclear encoded protein required for translation of COX1 mRNA; binds to Cox1 protein
YDR077W	0.21606	MSN4	YDR077W|SED1|S000002484|Major stress-induced structural GPI-cell wall glycoprotein in stationary-phase cells, associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites
YKR033C	0.214551	MSN4	YKR033C||S000001741|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene DAL80
YLR034C	0.213555	MSN4	YLR034C|SMF3|S000004024|Putative divalent metal ion transporter involved in iron homeostasis; transcriptionally regulated by metal ions; member of the Nramp family of metal transport proteins
YMR052W	0.213409	MSN4	YMR052W|FAR3|S000004656|Protein involved in G1 cell cycle arrest in response to pheromone, in a pathway different from the Far1p-dependent pathway; interacts with Far7p, Far8p, Far9p, Far10p, and Far11p
YGR126W	0.213003	MSN4	YGR126W||S000003358|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS
YGR232W	0.212898	MSN4	YGR232W|NAS6|S000003464|Regulatory, non-ATPase subunit of the 26S proteasome; homolog of the human oncoprotein gankyrin, which interacts with the retinoblastoma tumor suppressor (Rb) and cyclin-dependent kinase 4/6
YBL013W	0.211734	MSN4	YBL013W|FMT1|S000000109|Methionyl-tRNA formyltransferase, catalyzes the formylation of initiator Met-tRNA in mitochondria; potential Cdc28p substrate
YJL182C	0.21134	MSN4	YJL182C||S000003718|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps uncharacterized ORF YJL181W
YDL015C	0.208659	MSN4	YDL015C|TSC13|S000002173|Enoyl reductase that catalyzes the last step in each cycle of very long chain fatty acid elongation, localizes to the ER, highly enriched in a structure marking nuclear-vacuolar junctions, coimmunoprecipitates with elongases Fen1p and Sur4p
YIL007C	0.208477	MSN4	YIL007C|NAS2|S000001269|Protein with similarity to the p27 subunit of mammalian proteasome modulator; not essential; interacts with Rpn4p
YGR082W	0.208299	MSN4	YGR082W|TOM20|S000003314|Component of the TOM (translocase of outer membrane) complex responsible for recognition and initial import steps for all mitochondrially directed proteins; acts as a receptor for incoming precursor proteins
YIR018W	0.208279	MSN4	YIR018W|YAP5|S000001457|Basic leucine zipper (bZIP) transcription factor
YKR076W	0.206904	MSN4	YKR076W|ECM4|S000001784|Omega class glutathione transferase; not essential; similar to Ygr154cp; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YIL147C	0.205372	MSN4	YIL147C|SLN1|S000001409|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
YDR452W	0.204457	MSN4	YDR452W|PPN1|S000002860|Vacuolar endopolyphosphatase with a role in phosphate metabolism; functions as a homodimer
YOL023W	0.203854	MSN4	YOL023W|IFM1|S000005383|Mitochondrial translation initiation factor 2
YDR440W	0.203746	MSN4	YDR440W|DOT1|S000002848|Nucleosomal histone H3-Lys79 methylase, associates with transcriptionally active genes, functions in gene silencing at telomeres, most likely by directly modulating chromatin structure and Sir protein localization
YNR004W	0.203139	MSN4	YNR004W||S000005287|Putative protein of unknown function; haploid disruptant exhibits slow growth rate on glucose-minimal medium at 15 C
YGR191W	0.200442	MSN4	YGR191W|HIP1|S000003423|High-affinity histidine permease, also involved in the transport of manganese ions
YHR175W	0.198325	MSN4	YHR175W|CTR2|S000001218|Putative low-affinity copper transporter of the vacuolar membrane; mutation confers resistance to toxic copper concentrations, while overexpression confers resistance to copper starvation
YBR083W	0.196539	MSN4	YBR083W|TEC1|S000000287|Transcription factor required for full Ty1 epxression, Ty1-mediated gene activation, and haploid invasive and diploid pseudohyphal growth; TEA/ATTS DNA-binding domain family member
YKL188C	0.196082	MSN4	YKL188C|PXA2|S000001671|Subunit of a heterodimeric peroxisomal ATP-binding cassette transporter complex (Pxa1p-Pxa2p), required for import of long-chain fatty acids into peroxisomes; similarity to human adrenoleukodystrophy transporter and ALD-related proteins
YFR047C	0.195157	MSN4	YFR047C|BNA6|S000001943|Quinolinate phosphoribosyl transferase, required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p
YOR020W-A	0.194818	MSN4	YOR020W-A||S000028526|Putative protein of unknown function, conserved in A. gossypii; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER097W	0.194771	MSN4	YER097W||S000000899|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKL071W	0.194667	MSN4	YKL071W||S000001554|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDL190C	0.194209	MSN4	YDL190C|UFD2|S000002349|Ubiquitin chain assembly factor (E4) that cooperates with a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin protein ligase (E3) to conjugate ubiquitin to substrates; also functions as an E3
YML110C	0.193754	MSN4	YML110C|COQ5|S000004578|2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase, involved in ubiquinone (Coenzyme Q) biosynthesis; localizes to the matrix face of the mitochondrial inner membrane in a large complex with other ubiquinone biosynthetic enzymes
YNL337W	0.193444	MSN4	YNL337W||S000005281|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPR022C	0.193405	MSN4	YPR022C||S000006226|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS
YBR172C	0.192841	MSN4	YBR172C|SMY2|S000000376|Protein of unknown function involved in COPII vesicle formation; interacts with the Sec23p/Sec24p subcomplex; overexpression suppresses the temperature sensitivity of a myo2 mutant; has similarity to S. pombe Mpd2
YPR065W	0.191942	MSN4	YPR065W|ROX1|S000006269|Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity
YJL016W	0.191519	MSN4	YJL016W||S000003553|Putative protein of unknown function; GFP-fusion protein localizes to the cytoplasm; conserved in closely related Saccharomyces species
YNR047W	0.190351	MSN4	YNR047W||S000005330|Putative protein kinase that, when overexpressed, interferes with pheromone-induced growth arrest; localizes to the cytoplasm; potential Cdc28p substrate
YGR143W	0.190039	MSN4	YGR143W|SKN1|S000003375|Protein involved in sphingolipid biosynthesis; type II membrane protein with similarity to Kre6p
YPR115W	0.189848	MSN4	YPR115W|GCA1|S000006319|Pleckstrin homology domain containing protein proposed to function as a glycerol channel activator; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR093W	0.189137	MSN4	YDR093W|DNF2|S000002500|Aminophospholipid translocase (flippase) that localizes primarily to the plasma membrane; contributes to endocytosis, protein transport and cell polarity; type 4 P-type ATPase
YFL039C	0.188678	MSN4	YFL039C|ACT1|S000001855|Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions
YDR425W	0.18828	MSN4	YDR425W|SNX41|S000002833|Sorting nexin, involved in the retrieval of late-Golgi SNAREs from the post-Golgi endosome to the trans-Golgi network; interacts with Snx4p
YLR219W	0.187783	MSN4	YLR219W|MSC3|S000004209|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; msc3 mutants are defective in directing meiotic recombination events to homologous chromatids; potential Cdc28p substrate
YDL170W	0.18673	MSN4	YDL170W|UGA3|S000002329|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; localized to the nucleus
YJR103W	0.184568	MSN4	YJR103W|URA8|S000003864|Minor CTP synthase isozyme (see also URA7), catalyzes the ATP-dependent transfer of the amide nitrogen from glutamine to UTP, forming CTP, the final step in de novo biosynthesis of pyrimidines; involved in phospholipid biosynthesis
YCR026C	0.183247	MSN4	YCR026C|NPP1|S000000621|Nucleotide pyrophosphatase/phosphodiesterase family member; mediates extracellular nucleotide phosphate hydrolysis along with Npp2p and Pho5p; activity and expression enhanced during conditions of phosphate starvation
YGR184C	0.183246	MSN4	YGR184C|UBR1|S000003416|Ubiquitin-protein ligase (E3) that interacts with Rad6p/Ubc2p to ubiquitinate substrates of the N-end rule pathway; binds to the Rpn2p, Rpt1p, and Rpt6p proteins of the 19S particle of the 26S proteasome
YGR220C	0.183107	MSN4	YGR220C|MRPL9|S000003452|Mitochondrial ribosomal protein of the large subunit
YKL066W	0.182809	MSN4	YKL066W||S000001549|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene YNK1
YGR136W	0.182797	MSN4	YGR136W|LSB1|S000003368|Protein containing an N-terminal SH3 domain; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization
YPL089C	0.18265	MSN4	YPL089C|RLM1|S000006010|MADS-box transcription factor, component of the protein kinase C-mediated MAP kinase pathway involved in the maintenance of cell integrity; phosphorylated and activated by the MAP-kinase Slt2p
YDR314C	0.181951	MSN4	YDR314C|RAD34|S000002722|Protein involved in nucleotide excision repair (NER); homologous to RAD4
YNL242W	0.181701	MSN4	YNL242W|ATG2|S000005186|Peripheral membrane protein required for vesicle formation during autophagy, pexophagy, and the cytoplasm-to-vaucole targeting (Cvt) pathway; involved in Atg9p cycling between the pre-autophagosomal structure and mitochondria
YPR003C	0.180471	MSN4	YPR003C||S000006207|Putative sulfate permease; physically interacts with Hsp82p; green fluorescent protein (GFP)-fusion protein localizes to the ER; YPR003C is not an essential gene
YJL152W	0.180025	MSN4	YJL152W||S000003688|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YAL055W	0.179651	MSN4	YAL055W|PEX22|S000000051|Putative peroxisomal membrane protein required for import of peroxisomal proteins, functionally complements a Pichia pastoris pex22 mutation
YGL251C	0.179244	MSN4	YGL251C|HFM1|S000003220|Meiosis specific DNA helicase involved in the conversion of double-stranded breaks to later recombination intermediates and in crossover control; catalyzes the unwinding of Holliday junctions; has ssDNA and dsDNA stimulated ATPase activity
YML051W	0.178756	MSN4	YML051W|GAL80|S000004515|Transcriptional regulator involved in the repression of GAL genes in the absence of galactose; inhibits transcriptional activation by Gal4p; inhibition relieved by Gal3p or Gal1p binding
YDR431W	0.176405	MSN4	YDR431W||S000002839|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR513W	0.176226	MSN4	YDR513W|GRX2|S000002921|Cytoplasmic glutaredoxin, thioltransferase, glutathione-dependent disulfide oxidoreductase involved in maintaining redox state of target proteins, also exhibits glutathione peroxidase activity, expression induced in response to stress
YPL167C	0.176076	MSN4	YPL167C|REV3|S000006088|Catalytic subunit of DNA polymerase zeta, which is involved in DNA repair and translesion synthesis; required for mutagenesis induced by DNA damage
YPR064W	0.175941	MSN4	YPR064W||S000006268|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YJL165C	0.174138	MSN4	YJL165C|HAL5|S000003701|Putative protein kinase; overexpression increases sodium and lithium tolerance, whereas gene disruption increases cation and low pH sensitivity and impairs potassium uptake, suggesting a role in regulation of Trk1p and/or Trk2p transporters
YLR247C	0.17372	MSN4	YLR247C|IRC20|S000004237|Putative helicase; localizes to the mitochondrion and the nucleus; YLR247C is not an essential gene; null mutant displays increased levels of spontaneous Rad52p foci
YNL083W	0.172149	MSN4	YNL083W|SAL1|S000005027|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
YIL046W-A	0.169569	MSN4	YIL046W-A||S000028836|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YBR185C	0.169435	MSN4	YBR185C|MBA1|S000000389|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
YER091C-A	0.169379	MSN4	YER091C-A||S000007238|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR134W	0.167979	MSN4	YMR134W|ERG29|S000004741|Protein that binds to and regulates Erg25p; localized to the ER; null mutant is viable in a respiratory defective background; synthetic lethal with mmt1 and mmt2 mutations; highly conserved in ascomycetes
YER190W	0.167078	MSN4	YER190W|YRF1-2|S000000992|Helicase encoded by the Y' element of subtelomeric regions, highly expressed in the mutants lacking the telomerase component TLC1; potentially phosphorylated by Cdc28p; induced by treatment with 8-methoxypsoralen and UVA irradiation
YGR190C	0.166829	MSN4	YGR190C||S000003422|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene HIP1/YGR191W
YER087W	0.166662	MSN4	YER087W|AIM10|S000000889|Protein with similarity to tRNA synthetases; non-tagged protein is detected in purified mitochondria; null mutant displays decreased frequency of mitochondrial genome loss (petite formation), severe growth defect in minimal glycerol media
YJR117W	0.161578	MSN4	YJR117W|STE24|S000003878|Highly conserved zinc metalloprotease that functions in two steps of a-factor maturation, C-terminal CAAX proteolysis and the first step of N-terminal proteolytic processing; contains multiple transmembrane spans
YDR475C	0.159587	MSN4	YDR475C|JIP4|S000002883|Protein of unknown function; previously annotated as two separate ORFs, YDR474C and YDR475C, which were merged as a result of corrections to the systematic reference sequence
YJL079C	0.159204	MSN4	YJL079C|PRY1|S000003615|Protein of unknown function, has similarity to Pry2p and Pry3p and to the plant PR-1 class of pathogen related proteins
YDR426C	0.158886	MSN4	YDR426C||S000002834|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF SNX41
YGL229C	0.158716	MSN4	YGL229C|SAP4|S000003198|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
YPL234C	0.157927	MSN4	YPL234C|TFP3|S000006155|Vacuolar ATPase V0 domain subunit c', involved in proton transport activity; hydrophobic integral membrane protein (proteolipid) containing four transmembrane segments; N and C termini are in the vacuolar lumen
YJL094C	0.156433	MSN4	YJL094C|KHA1|S000003630|Putative K+/H+ antiporter with a probable role in intracellular cation homeostasis, localized to Golgi vesicles and detected in highly purified mitochondria in high-throughput studies
YML070W	0.155139	MSN4	YML070W|DAK1|S000004535|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YKR032W	0.15454	MSN4	YKR032W||S000001740|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR171W	0.15142	MSN4	YHR171W|ATG7|S000001214|Autophagy-related protein and dual specificity member of the E1 family of ubiquitin-activating enzymes; mediates the conjugation of Atg12p with Atg5p and Atg8p with phosphatidylethanolamine, required steps in autophagosome formation
YLL030C	0.151129	MSN4	YLL030C||S000003953|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR431C	0.149988	MSN4	YLR431C|ATG23|S000004423|Peripheral membrane protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway; cycles between the pre-autophagosome (PAS) and non-PAS locations; forms a complex with Atg9p and Atg27p
YPL071C	0.149865	MSN4	YPL071C||S000005992|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YOL058W	0.14984	MSN4	YOL058W|ARG1|S000005419|Arginosuccinate synthetase, catalyzes the formation of L-argininosuccinate from citrulline and L-aspartate in the arginine biosynthesis pathway; potential Cdc28p substrate
YOL052C	0.149567	MSN4	YOL052C|SPE2|S000005412|S-adenosylmethionine decarboxylase, required for the biosynthesis of spermidine and spermine; cells lacking Spe2p require spermine or spermidine for growth in the presence of oxygen but not when grown anaerobically
YBR082C	0.148837	MSN4	YBR082C|UBC4|S000000286|Ubiquitin-conjugating enzyme (E2), mediates degradation of short-lived and abnormal proteins; interacts with E3-CaM in ubiquitinating calmodulin; interacts with many SCF ubiquitin protein ligases; component of the cellular stress response
YFR012W	0.148517	MSN4	YFR012W||S000001908|Putative protein of unknown function
YFL041W-A	0.144677	MSN4	YFL041W-A||S000028547|Putative protein of unknown function; identified by fungal homology and RT-PCR
YCR050C	0.144214	MSN4	YCR050C||S000000646|Non-essential protein of unknown function; deletion mutant is synthetically sick or lethal with alpha-synuclein
YLR425W	0.143661	MSN4	YLR425W|TUS1|S000004417|Guanine nucleotide exchange factor (GEF) that functions to modulate Rho1p activity as part of the cell integrity signaling pathway; multicopy suppressor of tor2 mutation and ypk1 ypk2 double mutation; potential Cdc28p substrate
YKL121W	0.142942	MSN4	YKL121W||S000001604|Putative protein of unknown function
YCR063W	0.141309	MSN4	YCR063W|BUD31|S000000659|Protein involved in bud-site selection; analysis of integrated high-throughput datasets predicts an involvement in RNA splicing; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YOR316C-A	0.140956	MSN4	YOR316C-A||S000028584|Putative protein of unknown function; identified by fungal homology and RT-PCR
YDR143C	0.140899	MSN4	YDR143C|SAN1|S000002550|Ubiquitin-protein ligase, involved in the proteasome-dependent degradation of aberrant nuclear proteins
YLR052W	0.140214	MSN4	YLR052W|IES3|S000004042|Subunit of the INO80 chromatin remodeling complex
YJL101C	0.139475	MSN4	YJL101C|GSH1|S000003637|Gamma glutamylcysteine synthetase catalyzes the first step in glutathione (GSH) biosynthesis; expression induced by oxidants, cadmium, and mercury
YDL185C-A	0.139298	MSN4	YDL185C-A||S000007600|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDL185W; identified by homology with hemiascomycetous yeast species
YDR393W	0.138978	MSN4	YDR393W|SHE9|S000002801|Mitochondrial inner membrane protein required for normal mitochondrial morphology, may be involved in fission of the inner membrane; forms a homo-oligomeric complex
YIL120W	0.137754	MSN4	YIL120W|QDR1|S000001382|Multidrug transporter of the major facilitator superfamily, required for resistance to quinidine, ketoconazole, fluconazole, and barban
YCL039W	0.137456	MSN4	YCL039W|GID7|S000000544|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains six WD40 repeats; computational analysis suggests that Gid7p and Moh1p have similar functions
YBL101C	0.13713	MSN4	YBL101C|ECM21|S000000197|Non-essential protein of unknown function; promoter contains several Gcn4p binding elements
YPL088W	0.137012	MSN4	YPL088W||S000006009|Putative aryl alcohol dehydrogenase; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance
YOL009C	0.136707	MSN4	YOL009C|MDM12|S000005369|Mitochondrial outer membrane protein, required for transmission of mitochondria to daughter cells; component of the Mdm10-Mdm12-Mmm1 complex involved in import and assembly of outer membrane beta-barrel proteins
YMR008C	0.1365	MSN4	YMR008C|PLB1|S000004610|Phospholipase B (lysophospholipase) involved in lipid metabolism, required for deacylation of phosphatidylcholine and phosphatidylethanolamine but not phosphatidylinositol
YPL179W	0.135293	MSN4	YPL179W|PPQ1|S000006100|Putative protein serine/threonine phosphatase; null mutation enhances efficiency of translational suppressors
YPL257W	0.134952	MSN4	YPL257W||S000006178|Putative protein of unknown function;; homozygous diploid deletion strain exhibits low budding index; physically interacts with Hsp82p; YPL257W is not an essential gene
YJL112W	0.134783	MSN4	YJL112W|MDV1|S000003648|Peripheral protein of the cytosolic face of the mitochondrial outer membrane, required for mitochondrial fission; interacts with Fis1p and with the dynamin-related GTPase Dnm1p; contains WD repeats
YLR035C	0.134653	MSN4	YLR035C|MLH2|S000004025|Protein involved in the mismatch repair of certain frameshift intermediates and involved in meiotic recombination; forms a complex with Mlh1p
YNL019C	0.134624	MSN4	YNL019C||S000004964|Putative protein of unknown function
YCR049C	0.134487	MSN4	YCR049C||S000000645|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJL110C	0.133582	MSN4	YJL110C|GZF3|S000003646|GATA zinc finger protein and Dal80p homolog that negatively regulates nitrogen catabolic gene expression by competing with Gat1p for GATA site binding; function requires a repressive carbon source; dimerizes with Dal80p and binds to Tor1p
YDL089W	0.132679	MSN4	YDL089W||S000002247|Protein of unknown function; interacts with meiotic division protein Csm1p; green fluorescent protein (GFP)-fusion protein localizes to the nuclear periphery, potential Cdc28p substrate
YOR020C	0.131946	MSN4	YOR020C|HSP10|S000005546|Mitochondrial matrix co-chaperonin that inhibits the ATPase activity of Hsp60p, a mitochondrial chaperonin; involved in protein folding and sorting in the mitochondria; 10 kD heat shock protein with similarity to E. coli groES
YIL036W	0.131743	MSN4	YIL036W|CST6|S000001298|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, activates transcription of genes involved in utilization of non-optimal carbon sources; involved in telomere maintenance
YAL027W	0.129886	MSN4	YAL027W|SAW1|S000000025|Catalyzes 3'-nonhomologous tail removal of Rad1p/Rad10p-dependent single-strand annealing recombination intermediates; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YAL027W is a non-essential gene
YFR040W	0.12918	MSN4	YFR040W|SAP155|S000001936|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, Sap185p, and Sap190p
YDL233W	0.128691	MSN4	YDL233W||S000002392|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YDL233W is not an essential gene
YML129C	0.128125	MSN4	YML129C|COX14|S000004598|Mitochondrial membrane protein, involved in translational regulation of Cox1p and assembly of cytochrome c oxidase (complex IV); associates with complex IV assembly intermediates and complex III/complex IV supercomplexes
YOR095C	0.127531	MSN4	YOR095C|RKI1|S000005621|Ribose-5-phosphate ketol-isomerase, catalyzes the interconversion of ribose 5-phosphate and ribulose 5-phosphate in the pentose phosphate pathway; participates in pyridoxine biosynthesis
YIL050W	0.127115	MSN4	YIL050W|PCL7|S000001312|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
YNL167C	0.126628	MSN4	YNL167C|SKO1|S000005111|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, forms a complex with Tup1p and Ssn6p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses
YLR241W	0.124993	MSN4	YLR241W||S000004231|Putative protein of unknown function, may be involved in detoxification
YBR220C	0.124743	MSN4	YBR220C||S000000424|Putative protein of unknown function; YBR220C is not an essential gene
YLR390W	0.123962	MSN4	YLR390W|ECM19|S000004382|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YJR059W	0.122586	MSN4	YJR059W|PTK2|S000003820|Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake
YHR131W-A	0.121262	MSN4	YHR131W-A||S000028782|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YHR131C
YNL007C	0.121148	MSN4	YNL007C|SIS1|S000004952|Type II HSP40 co-chaperone that interacts with the HSP70 protein Ssa1p; not functionally redundant with Ydj1p due to due to substrate specificity; shares similarity with bacterial DnaJ proteins
YBR255W	0.120744	MSN4	YBR255W|MTC4|S000000459|Protein of unknown function, required for normal growth rate at 15 degrees C; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YBR255W is synthetically sick with cdc13-1
YBL033C	0.120151	MSN4	YBL033C|RIB1|S000000129|GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway
YDL061C	0.119769	MSN4	YDL061C|RPS29B|S000002219|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps29Ap and has similarity to rat S29 and E. coli S14 ribosomal proteins
YOR136W	0.118109	MSN4	YOR136W|IDH2|S000005662|Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle; phosphorylated
YOL116W	0.117914	MSN4	YOL116W|MSN1|S000005476|Transcriptional activator involved in regulation of invertase and glucoamylase expression, invasive growth and pseudohyphal differentiation, iron uptake, chromium accumulation, and response to osmotic stress; localizes to the nucleus
YIR038C	0.117871	MSN4	YIR038C|GTT1|S000001477|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
YIL105C	0.117787	MSN4	YIL105C|SLM1|S000001367|Phosphoinositide PI4,5P(2) binding protein, forms a complex with Slm2p; acts downstream of Mss4p in a pathway regulating actin cytoskeleton organization in response to stress; subunit of and phosphorylated by the TORC2 complex
YGR101W	0.116851	MSN4	YGR101W|PCP1|S000003333|Mitochondrial serine protease required for the processing of various mitochondrial proteins and maintenance of mitochondrial DNA and morphology; belongs to the rhomboid-GlpG superfamily of intramembrane peptidases
YKL061W	0.113836	MSN4	YKL061W||S000001544|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endosome
YML109W	0.111993	MSN4	YML109W|ZDS2|S000004577|Protein that interacts with silencing proteins at the telomere, involved in transcriptional silencing; paralog of Zds1p
YLL025W	0.109059	MSN4	YLL025W|PAU17|S000003948|Putative protein of unknown function; YLL025W is not an essential gene
YLL010C	0.106834	MSN4	YLL010C|PSR1|S000003933|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
YBL093C	0.106829	MSN4	YBL093C|ROX3|S000000189|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme
YPR138C	0.105535	MSN4	YPR138C|MEP3|S000006342|Ammonium permease of high capacity and low affinity; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation ammonia permease
YER095W	0.104653	MSN4	YER095W|RAD51|S000000897|Strand exchange protein, forms a helical filament with DNA that searches for homology; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; homolog of Dmc1p and bacterial RecA protein
YDL025C	0.104572	MSN4	YDL025C||S000002183|Putative protein kinase, potentially phosphorylated by Cdc28p; YDL025C is not an essential gene
YGR161W-C	0.104443	MSN4	YGR161W-C||S000029726|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YFL023W	0.102908	MSN4	YFL023W|BUD27|S000001871|Protein involved in bud-site selection, nutrient signaling, and gene expression controlled by TOR kinase; diploid mutants show a random budding pattern rather than the wild-type bipolar pattern; plays a role in regulating Ty1 transposition
YBR109W-A	0.102465	MSN4	YBR109W-A||S000028737|Putative protein of unknown function; questionable ORF from MIPS
YDR409W	0.102311	MSN4	YDR409W|SIZ1|S000002817|SUMO/Smt3 ligase that promotes the attachment of sumo (Smt3p; small ubiquitin-related modifier) to proteins; binds Ubc9p and may bind septins; specifically required for sumoylation of septins in vivo; localized to the septin ring
YNL073W	0.10213	MSN4	YNL073W|MSK1|S000005017|Mitochondrial lysine-tRNA synthetase, required for import of both aminoacylated and deacylated forms of tRNA(Lys) into mitochondria
YIL012W	0.101191	MSN4	YIL012W||S000001274|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YFR045W	0.100006	MSN4	YFR045W||S000001941|Putative mitochondrial transport protein; null mutant is viable, exhibits decreased levels of chitin and normal resistance to calcofluor white
YHR161C	0.0996031	MSN4	YHR161C|YAP1801|S000001204|Protein involved in clathrin cage assembly; binds Pan1p and clathrin; homologous to Yap1802p, member of the AP180 protein family
YHR146W	0.0958115	MSN4	YHR146W|CRP1|S000001189|Protein that binds to cruciform DNA structures
YNL215W	0.0951332	MSN4	YNL215W|IES2|S000005159|Protein that associates with the INO80 chromatin remodeling complex under low-salt conditions
YGR112W	0.094081	MSN4	YGR112W|SHY1|S000003344|Mitochondrial inner membrane protein required for assembly of cytochrome c oxidase (complex IV); associates with complex IV assembly intermediates and complex III/complex IV supercomplexes; similar to human SURF1 involved in Leigh Syndrome
YKR044W	0.0939875	MSN4	YKR044W|UIP5|S000001752|Protein of unknown function that interacts with Ulp1p, a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates
YJL022W	0.0939311	MSN4	YJL022W||S000003559|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene PET130
YDL162C	0.0936561	MSN4	YDL162C||S000002321|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps ENT1/YDL161W, a verified gene involved in endocytosis and actin cortical patch assembly
YJL133W	0.0920513	MSN4	YJL133W|MRS3|S000003669|Mitochondrial iron transporter of the mitochondrial carrier family (MCF), very similar to and functionally redundant with Mrs4p; functions under low-iron conditions; may transport other cations in addition to iron
YJR052W	0.0917751	MSN4	YJR052W|RAD7|S000003813|Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad16p) during nucleotide excision repair; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex
YDR374W-A	0.0914704	MSN4	YDR374W-A||S000113553|Putative protein of unknown function
YAL037W	0.0912588	MSN4	YAL037W||S000000035|Putative protein of unknown function
YOR278W	0.0911671	MSN4	YOR278W|HEM4|S000005804|Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway
YNL046W	0.0895718	MSN4	YNL046W||S000004991|Putative protein of unknown function; expression depends on Swi5p; GFP-fusion protein localizes to the endoplasmic reticulum; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO)
YAL066W	0.0888659	MSN4	YAL066W||S000000061|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL328C	0.0887539	MSN4	YNL328C|MDJ2|S000005272|Constituent of the mitochondrial import motor associated with the presequence translocase; function overlaps with that of Pam18p; stimulates the ATPase activity of Ssc1p to drive mitochondrial import; contains a J domain
YIL013C	0.0876479	MSN4	YIL013C|PDR11|S000001275|ATP-binding cassette (ABC) transporter, multidrug transporter involved in multiple drug resistance; mediates sterol uptake when sterol biosynthesis is compromisedregulated by Pdr1p; required for anaerobic growth
YKL159C	0.0873906	MSN4	YKL159C|RCN1|S000001642|Protein involved in calcineurin regulation during calcium signaling; has similarity to H. sapiens DSCR1 which is found in the Down Syndrome candidate region
YPL162C	0.0867877	MSN4	YPL162C||S000006083|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of vacuole with cell cycle-correlated morphology
YKR065C	0.0863168	MSN4	YKR065C|PAM17|S000001773|Presequence translocase-associated motor subunit, required for stable complex formation between cochaperones Pam16p and Pam18p, promotes association of Pam16p-Pam18p with the presequence translocase
YCL009C	0.0862401	MSN4	YCL009C|ILV6|S000000515|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
YJR030C	0.0861427	MSN4	YJR030C||S000003791|Putative protein of unknown function; expression repressed in carbon limited vs carbon replete chemostat cultures; YJR030C is a non-essential gene
YOR135C	0.085325	MSN4	YOR135C|IRC14|S000005661|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YOR136W; null mutant displays increased levels of spontaneous Rad52 foci
YKL157W	0.0844945	MSN4	YKL157W|APE2|S000001640|Zinc-dependent metallopeptidase yscII, may have a role in obtaining leucine from dipeptide substrates; sequence coordinates have changed since RT-PCR analysis showed that the adjacent ORF YKL158W comprises the 5' exon of APE2/YKL157W
YNL244C	0.08344	MSN4	YNL244C|SUI1|S000005188|Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase
YLR218C	0.0833284	MSN4	YLR218C||S000004208|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YLR218C is not essential; mutants exhibit glycogen storage defects and growth defects on a non-fermentable carbon source
YOL004W	0.0826943	MSN4	YOL004W|SIN3|S000005364|Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity
YJR116W	0.0817044	MSN4	YJR116W||S000003877|Putative protein of unknown function
YMR030W	0.079843	MSN4	YMR030W|RSF1|S000004632|Protein required for respiratory growth; localized to both the nucleus and mitochondrion; mutant displays decreased transcription of specific nuclear and mitochondrial genes whose products are involved in respiratory growth
YPR159W	0.077351	MSN4	YPR159W|KRE6|S000006363|Protein required for beta-1,6 glucan biosynthesis; putative beta-glucan synthase; appears functionally redundant with Skn1p
YHR118C	0.0772606	MSN4	YHR118C|ORC6|S000001160|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; phosphorylated by Cdc28p
YNL201C	0.0771744	MSN4	YNL201C|PSY2|S000005145|Putative subunit of an evolutionarily conserved protein phosphatase complex containing the catalytic subunit Pph3p and the regulatory subunit Psy4p; required for cisplatin and oxaliplatin resistance; localizes to nucleus
YDR445C	0.0769541	MSN4	YDR445C||S000002853|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR222C	0.0768702	MSN4	YMR222C|FSH2|S000004835|Serine hydrolase that localizes to the cytoplasm; sequence is similar to Fsh1p and Fsh3p
YIL144W	0.0768104	MSN4	YIL144W|TID3|S000001406|Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering
YNL124W	0.0766498	MSN4	YNL124W|NAF1|S000005068|Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins
YDR268W	0.0764102	MSN4	YDR268W|MSW1|S000002676|Mitochondrial tryptophanyl-tRNA synthetase
YLR248W	0.0751519	MSN4	YLR248W|RCK2|S000004238|Protein kinase involved in the response to oxidative and osmotic stress; identified as suppressor of S. pombe cell cycle checkpoint mutations
YPL140C	0.0729821	MSN4	YPL140C|MKK2|S000006061|Mitogen-activated kinase kinase involved in protein kinase C signaling pathway that controls cell integrity; upon activation by Bck1p phosphorylates downstream target, Slt2p; functionally redundant with Mkk1p
YIL156W	0.0729406	MSN4	YIL156W|UBP7|S000001418|Ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YLR027C	0.0722888	MSN4	YLR027C|AAT2|S000004017|Cytosolic aspartate aminotransferase, involved in nitrogen metabolism; localizes to peroxisomes in oleate-grown cells
YNR060W	0.0716489	MSN4	YNR060W|FRE4|S000005343|Ferric reductase, reduces a specific subset of siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YCR073C	0.0715551	MSN4	YCR073C|SSK22|S000000669|MAP kinase kinase kinase of the HOG1 mitogen-activated signaling pathway; functionally redundant with, and homologous to, Ssk2p; interacts with and is activated by Ssk1p; phosphorylates Pbs2p
YJL127C	0.071141	MSN4	YJL127C|SPT10|S000003663|Putative histone acetylase, sequence-specific activator of histone genes, binds specifically and highly cooperatively to pairs of UAS elements in core histone promoters, functions at or near the TATA box
YGR031W	0.0691098	MSN4	YGR031W||S000003263|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER040W	0.0691012	MSN4	YER040W|GLN3|S000000842|Transcriptional activator of genes regulated by nitrogen catabolite repression (NCR), localization and activity regulated by quality of nitrogen source
YML048W	0.0684921	MSN4	YML048W|GSF2|S000004511|ER localized integral membrane protein that may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression
YJL210W	0.0679686	MSN4	YJL210W|PEX2|S000003746|RING-finger peroxin, peroxisomal membrane protein with a C-terminal zinc-binding RING domain, forms translocation subcomplex with Pex10p and Pex12p which functions in peroxisomal matrix protein import
YPL116W	0.0667334	MSN4	YPL116W|HOS3|S000006037|Trichostatin A-insensitive homodimeric histone deacetylase (HDAC) with specificity in vitro for histones H3, H4, H2A, and H2B; similar to Hda1p, Rpd3p, Hos1p, and Hos2p; deletion results in increased histone acetylation at rDNA repeats
YBL067C	0.0663512	MSN4	YBL067C|UBP13|S000000163|Putative ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YHR110W	0.0638965	MSN4	YHR110W|ERP5|S000001152|Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport
YKR052C	0.063474	MSN4	YKR052C|MRS4|S000001760|Mitochondrial iron transporter of the mitochondrial carrier family (MCF), very similar to and functionally redundant with Mrs3p; functions under low-iron conditions; may transport other cations in addition to iron
YGL127C	0.0631562	MSN4	YGL127C|SOH1|S000003095|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; involved in telomere maintenance; conserved with other metazoan MED31 subunits
YMR292W	0.062573	MSN4	YMR292W|GOT1|S000004906|Evolutionarily conserved non-essential protein present in early Golgi cisternae that may be involved in ER-Golgi transport at a step after vesicle tethering to Golgi membranes, exhibits membrane topology similar to that of Sft2p
YJL023C	0.0621527	MSN4	YJL023C|PET130|S000003560|Protein required for respiratory growth; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR191W	0.0615086	MSN4	YDR191W|HST4|S000002599|Member of the Sir2 family of NAD(+)-dependent protein deacetylases; involved along with Hst3p in silencing at telomeres, cell cycle progression, radiation resistance, genomic stability and short-chain fatty acid metabolism
YER181C	0.0608838	MSN4	YER181C||S000000983|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative data; extensively overlaps a Ty1 LTR; protein product is detected in highly purified mitochondria in high-throughput studies
YKR014C	0.0600344	MSN4	YKR014C|YPT52|S000001722|GTPase, similar to Ypt51p and Ypt53p and to mammalian rab5; required for vacuolar protein sorting and endocytosis
YHR119W	0.0595554	MSN4	YHR119W|SET1|S000001161|Histone methyltransferase, subunit of the COMPASS (Set1C) complex which methylates histone H3 on lysine 4; required in transcriptional silencing near telomeres and at the silent mating type loci; contains a SET domain
YFR011C	0.0593902	MSN4	YFR011C|AIM13|S000001907|Putative protein of unknown function; non-tagged protein is detected in highly purified mitochondria; null mutant displays increased frequency of mitochondrial genome loss (petite formation) and reduced growth rate in minimal glycerol media
YPR080W	0.0583031	MSN4	YPR080W|TEF1|S000006284|Translational elongation factor EF-1 alpha; also encoded by TEF2; functions in the binding reaction of aminoacyl-tRNA (AA-tRNA) to ribosomes
YLR040C	0.0577936	MSN4	YLR040C||S000004030|Putative protein of unknown function; localizes to the cell wall; predicted to be a GPI-attached protein; upregulated by Mcm1p-Alpha1p transcription factor; partially overlaps the dubious ORF YLR041W; YLR040C is not essential
YCR084C	0.0571719	MSN4	YCR084C|TUP1|S000000680|General repressor of transcription, forms complex with Cyc8p, involved in the establishment of repressive chromatin structure through interactions with histones H3 and H4, appears to enhance expression of some genes
YOR358W	0.0568266	MSN4	YOR358W|HAP5|S000005885|Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; required for assembly and DNA binding activity of the complex
YJR062C	0.0565015	MSN4	YJR062C|NTA1|S000003823|Amidase, removes the amide group from N-terminal asparagine and glutamine residues to generate proteins with N-terminal aspartate and glutamate residues that are targets of ubiquitin-mediated degradation
YML057W	0.0563593	MSN4	YML057W|CMP2|S000004521|Calcineurin A; one isoform (the other is CNA1) of the catalytic subunit of calcineurin, a Ca++/calmodulin-regulated protein phosphatase which regulates Crz1p (a stress-response transcription factor), the other calcineurin subunit is CNB1
YGL185C	0.0552011	MSN4	YGL185C||S000003153|Putative protein with sequence similarity to hydroxyacid dehydrogenases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YCR032W	0.0539618	MSN4	YCR032W|BPH1|S000000628|PProtein homologous to human Chediak-Higashi syndrome and murine Beige proteins, which are implicated in disease syndromes due to defective lysosomal trafficking; mutant phenotype and genetic interactions suggest a role in protein sorting
YPL117C	0.0533391	MSN4	YPL117C|IDI1|S000006038|Isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase), catalyzes an essential activation step in the isoprenoid biosynthetic pathway; required for viability
YDL060W	0.0531392	MSN4	YDL060W|TSR1|S000002218|Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles
YPR066W	0.0527418	MSN4	YPR066W|UBA3|S000006270|Protein that acts together with Ula1p to activate Rub1p before its conjugation to proteins (neddylation), which may play a role in protein degradation; GFP-fusion protein localizes to the cytoplasm in a punctate pattern
YDR174W	0.0512254	MSN4	YDR174W|HMO1|S000002581|Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase
YKL050C	0.0511506	MSN4	YKL050C||S000001533|Protein of unknown function; the YKL050W protein is a target of the SCFCdc4 ubiquitin ligase complex and YKL050W transcription is regulated by Azf1p
YJR055W	0.0502581	MSN4	YJR055W|HIT1|S000003816|Protein of unknown function, required for growth at high temperature
YML130C	0.0502052	MSN4	YML130C|ERO1|S000004599|Thiol oxidase required for oxidative protein folding in the endoplasmic reticulum
YNL047C	0.0499613	MSN4	YNL047C|SLM2|S000004992|Phosphoinositide PI4,5P(2) binding protein, forms a complex with Slm1p; acts downstream of Mss4p in a pathway regulating actin cytoskeleton organization in response to stress; subunit of and phosphorylated by the TORC2 complex
YBR219C	0.0497637	MSN4	YBR219C||S000000423|Putative protein of unknown function; YBR219C is not an essential gene
YOR068C	0.0494592	MSN4	YOR068C|VAM10|S000005594|Protein involved in vacuole morphogenesis; acts at an early step of homotypic vacuole fusion that is required for vacuole tethering
YOL105C	0.0492885	MSN4	YOL105C|WSC3|S000005465|Partially redundant sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway involved in maintenance of cell wall integrity; involved in the response to heat shock and other stressors; regulates 1,3-beta-glucan synthesis
YFR016C	0.0489757	MSN4	YFR016C||S000001912|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and bud; interacts with Spa2p; YFL016C is not an essential gene
YCR017C	0.0488634	MSN4	YCR017C|CWH43|S000000610|Putative sensor/transporter protein involved in cell wall biogenesis; contains 14-16 transmembrane segments and several putative glycosylation and phosphorylation sites; null mutation is synthetically lethal with pkc1 deletion
YLR041W	0.0482511	MSN4	YLR041W||S000004031|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YLR040C
YMR160W	0.0481219	MSN4	YMR160W||S000004770|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of the vacuole; mutant has enhanced sensitivity to overexpression of mutant huntingtin; YMR160W is not an essential gene
YBR110W	0.0474711	MSN4	YBR110W|ALG1|S000000314|Mannosyltransferase, involved in asparagine-linked glycosylation in the endoplasmic reticulum (ER); essential for viability, mutation is functionally complemented by human ortholog
YDR229W	0.0458536	MSN4	YDR229W|IVY1|S000002637|Phospholipid-binding protein that interacts with both Ypt7p and Vps33p, may partially counteract the action of Vps33p and vice versa, localizes to the rim of the vacuole as cells approach stationary phase
YNL293W	0.0453067	MSN4	YNL293W|MSB3|S000005237|GTPase-activating protein for Sec4p and several other Rab GTPases, regulates exocytosis via its action on Sec4p, also required for proper actin organization; similar to Msb4p; both Msb3p and Msb4p localize to sites of polarized growth
YGR109C	0.0444064	MSN4	YGR109C|CLB6|S000003341|B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1
YNL071W	0.0442237	MSN4	YNL071W|LAT1|S000005015|Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex, which catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA
YPL233W	0.0432146	MSN4	YPL233W|NSL1|S000006154|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
YDR076W	0.0428393	MSN4	YDR076W|RAD55|S000002483|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
YLR354C	0.0416936	MSN4	YLR354C|TAL1|S000004346|Transaldolase, enzyme in the non-oxidative pentose phosphate pathway; converts sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to erythrose 4-phosphate and fructose 6-phosphate
YLL063C	0.0400258	MSN4	YLL063C|AYT1|S000003986|Acetyltransferase; catalyzes trichothecene 3-O-acetylation, suggesting a possible role in trichothecene biosynthesis
YFR057W	0.0395028	MSN4	YFR057W||S000001953|Putative protein of unknown function
YKL134C	0.0394148	MSN4	YKL134C|OCT1|S000001617|Mitochondrial intermediate peptidase, cleaves N-terminal residues of a subset of proteins upon import, after their cleavage by mitochondrial processing peptidase (Mas1p-Mas2p); may contribute to mitochondrial iron homeostasis
YKL165C-A	0.0390897	MSN4	YKL165C-A||S000007617|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPR100W	0.03856	MSN4	YPR100W|MRPL51|S000006304|Mitochondrial ribosomal protein of the large subunit
YDL001W	0.0382685	MSN4	YDL001W|RMD1|S000002159|Cytoplasmic protein required for sporulation
YCR001W	0.0375352	MSN4	YCR001W||S000000594|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YCR001W is not an essential gene
YNL062C	0.0368654	MSN4	YNL062C|GCD10|S000005006|Subunit of tRNA (1-methyladenosine) methyltransferase with Gcd14p, required for the modification of the adenine at position 58 in tRNAs, especially tRNAi-Met; first identified as a negative regulator of GCN4 expression
YGR233C	0.0368052	MSN4	YGR233C|PHO81|S000003465|Cyclin-dependent kinase (CDK) inhibitor, regulates Pho80p-Pho85p and Pcl7p-Pho85p cyclin-CDK complexes in response to phosphate levels; inhibitory activity for Pho80p-Pho85p requires myo-D-inositol heptakisphosphate (IP7) generated by Vip1p
YIL073C	0.0361419	MSN4	YIL073C|SPO22|S000001335|Meiosis-specific protein essential for chromosome synapsis, involved in completion of nuclear divisions during meiosis; induced early in meiosis
YKL003C	0.034665	MSN4	YKL003C|MRP17|S000001486|Mitochondrial ribosomal protein of the small subunit; MRP17 exhibits genetic interactions with PET122, encoding a COX3-specific translational activator
YOL018C	0.0343317	MSN4	YOL018C|TLG2|S000005378|Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation
YER084W-A	0.0332135	MSN4	YER084W-A||S000028752|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL054W	0.0330806	MSN4	YNL054W|VAC7|S000004999|Integral vacuolar membrane protein involved in vacuole inheritance and morphology; activates Fab1p kinase activity under basal conditions and also after hyperosmotic shock
YCL057W	0.0321232	MSN4	YCL057W|PRD1|S000000562|Zinc metalloendopeptidase, found in the cytoplasm and intermembrane space of mitochondria; with Cym1p, involved in degradation of mitochondrial proteins and of presequence peptides cleaved from imported proteins
YDL046W	0.0319893	MSN4	YDL046W|NPC2|S000002204|Functional homolog of human NPC2/He1, which is a cholesterol-binding protein whose deficiency causes Niemann-Pick type C2 disease involving retention of cholesterol in lysosomes
YJL027C	0.031484	MSN4	YJL027C||S000003564|Putative protein of unknown function
YHR022C	0.0310083	MSN4	YHR022C||S000001064|Putative protein of unknown function; YHR022C is not an essential gene.
YPL125W	0.028699	MSN4	YPL125W|KAP120|S000006046|Karyopherin with a role in the assembly or export of 60S ribosomal subunits
YER008C	0.0280154	MSN4	YER008C|SEC3|S000000810|Non-essential subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, Exo84p) which mediates targeting of post-Golgi vesicles to sites of active exocytosis; Sec3p specifically is a spatial landmark for secretion
YLR204W	0.0267496	MSN4	YLR204W|QRI5|S000004194|Mitochondrial inner membrane protein, required for accumulation of spliced COX1 mRNA; may have an additional role in translation of COX1 mRNA
YLL031C	0.0263724	MSN4	YLL031C|GPI13|S000003954|ER membrane localized phosphoryltransferase that adds phosphoethanolamine onto the third mannose residue of the glycosylphosphatidylinositol (GPI) anchor precursor; similar to human PIG-O protein
YER178W	0.0259288	MSN4	YER178W|PDA1|S000000980|E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex, catalyzes the direct oxidative decarboxylation of pyruvate to acetyl-CoA; phosphorylated; regulated by glucose
YER030W	0.0247432	MSN4	YER030W|CHZ1|S000000832|Histone chaperone for Htz1p/H2A-H2B dimer; required for the stabilization of the Chz1p-Htz1-H2B complex; has overlapping function with Nap1p; null mutant displays weak sensitivity to MMS and benomyl; contains a highly conserved CHZ motif
YKL058W	0.0246232	MSN4	YKL058W|TOA2|S000001541|TFIIA small subunit; involved in transcriptional activation, acts as antirepressor or as coactivator; homologous to smallest subunit of human and Drosophila TFIIA
YDL161W	0.0241263	MSN4	YDL161W|ENT1|S000002320|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
YHL010C	0.024081	MSN4	YHL010C|BRP2|S000001002|Putative protein of unknown function, contains a zinc finger region and has homology to human BRAP2, which is a cytoplasmic protein that binds nuclear localization sequences
YMR086W	0.0238851	MSN4	YMR086W||S000004692|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; cAMP represses YMR086W expression
YPL232W	0.023657	MSN4	YPL232W|SSO1|S000006153|Plasma membrane t-SNARE involved in fusion of secretory vesicles at the plasma membrane and in vesicle fusion during sporulation; forms a complex with Sec9p that binds v-SNARE Snc2p; syntaxin homolog; functionally redundant with Sso2p
YFR020W	0.0232552	MSN4	YFR020W||S000001916|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL045C	0.0231072	MSN4	YDL045C|FAD1|S000002203|Flavin adenine dinucleotide (FAD) synthetase, performs the second step in synthesis of FAD from riboflavin
YIL029W-A	0.0228192	MSN4	YIL029W-A||S000028788|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPR099C	0.0216807	MSN4	YPR099C||S000006303|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene MRPL51/YPR100W
YDR484W	0.0214944	MSN4	YDR484W|VPS52|S000002892|Component of the GARP (Golgi-associated retrograde protein) complex, Vps51p-Vps52p-Vps53p-Vps54p, which is required for the recycling of proteins from endosomes to the late Golgi; involved in localization of actin and chitin
YPR086W	0.0203527	MSN4	YPR086W|SUA7|S000006290|Transcription factor TFIIB, a general transcription factor required for transcription initiation and start site selection by RNA polymerase II
YPL158C	0.0203081	MSN4	YPL158C|AIM44|S000006079|Protein of unknown function; null mutant displays increased frequency of mitochondrial genome loss (petite formation) and reduced growth rate in minimal glycerol media
YNL306W	0.0198288	MSN4	YNL306W|MRPS18|S000005250|Mitochondrial ribosomal protein of the small subunit; essential for viability, unlike most other mitoribosomal proteins
YDR068W	0.0193048	MSN4	YDR068W|DOS2|S000002475|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YKR106W	0.0188154	MSN4	YKR106W||S000001814|Protein of unconfirmed function; displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins; coding sequence 98% identical to that of YCL073C
YHR131C	0.0183637	MSN4	YHR131C||S000001173|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR029W	0.0181793	MSN4	YDR029W||S000002436|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YGR111W	0.0178077	MSN4	YGR111W||S000003343|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YGL098W	0.0169733	MSN4	YGL098W|USE1|S000003066|Essential SNARE protein localized to the ER, involved in retrograde traffic from the Golgi to the ER; forms a complex with the SNAREs Sec22p, Sec20p and Ufe1p
YIR006C	0.0164149	MSN4	YIR006C|PAN1|S000001445|Part of actin cytoskeleton-regulatory complex Pan1p-Sla1p-End3p, associates with actin patches on the cell cortex; promotes protein-protein interactions essential for endocytosis; previously thought to be a subunit of poly(A) ribonuclease
YLR256W	0.0164106	MSN4	YLR256W|HAP1|S000004246|Zinc finger transcription factor involved in the complex regulation of gene expression in response to levels of heme and oxygen; the S288C sequence differs from other strain backgrounds due to a Ty1 insertion in the carboxy terminus
YGL197W	0.0161162	MSN4	YGL197W|MDS3|S000003165|Protein with an N-terminal kelch-like domain, putative negative regulator of early meiotic gene expression; required, with Pmd1p, for growth under alkaline conditions
YBR024W	0.0154005	MSN4	YBR024W|SCO2|S000000228|Protein anchored to the mitochondrial inner membrane, similar to Sco1p and may have a redundant function with Sco1p in delivery of copper to cytochrome c oxidase; interacts with Cox2p
YGR224W	0.014727	MSN4	YGR224W|AZR1|S000003456|Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs such as ketoconazole and fluconazole
YGL150C	0.0142103	MSN4	YGL150C|INO80|S000003118|ATPase that forms a large complex, containing actin and several actin-related proteins, that has chromatin remodeling activity and 3' to 5' DNA helicase activity in vitro; shows similarity to the Snf2p family of ATPases
YDL052C	0.0128814	MSN4	YDL052C|SLC1|S000002210|1-acyl-sn-gylcerol-3-phosphate acyltransferase, catalyzes the acylation of lysophosphatidic acid to form phosphatidic acid, a key intermediate in lipid metabolism; enzymatic activity detected in lipid particles and microsomes
YDL126C	0.0125689	MSN4	YDL126C|CDC48|S000002284|ATPase in ER, nuclear membrane and cytosol with homology to mammalian p97; in a complex with Npl4p and Ufd1p participates in retrotranslocation of ubiquitinated proteins from the ER into the cytosol for degradation by the proteasome
YNL004W	0.0121123	MSN4	YNL004W|HRB1|S000004949|Poly(A+) RNA-binding protein, involved in the export of mRNAs from the nucleus to the cytoplasm; similar to Gbp2p and Npl3p
YIL145C	0.0117025	MSN4	YIL145C|PAN6|S000001407|Pantothenate synthase, also known as pantoate-beta-alanine ligase, required for pantothenic acid biosynthesis, deletion causes pantothenic acid auxotrophy, homologous to E. coli panC
YOL164W	0.0116244	MSN4	YOL164W|BDS1|S000005524|Bacterially-derived sulfatase required for use of alkyl- and aryl-sulfates as sulfur sources
YAR003W	0.0107314	MSN4	YAR003W|SWD1|S000000064|Subunit of the COMPASS (Set1C) complex, which methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; WD40 beta propeller superfamily member with similarity to mammalian Rbbp7
YML114C	0.0102798	MSN4	YML114C|TAF8|S000004582|TFIID subunit (65 kDa), involved in RNA polymerase II transcription initiation
YKL002W	0.00861853	MSN4	YKL002W|DID4|S000001485|Class E Vps protein of the ESCRT-III complex, required for sorting of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to the vacuole, involved in endocytosis
YOR008C	0.00841018	MSN4	YOR008C|SLG1|S000005534|Sensor-transducer of the stress-activated PKC1-MPK1 kinase pathway involved in maintenance of cell wall integrity; involved in organization of the actin cytoskeleton; secretory pathway Wsc1p is required for the arrest of secretion response
YIL001W	0.00488195	MSN4	YIL001W||S000001263|Hypothetical protein
YGR231C	0.00487943	MSN4	YGR231C|PHB2|S000003463|Subunit of the prohibitin complex (Phb1p-Phb2p), a 1.2 MDa ring-shaped inner mitochondrial membrane chaperone that stabilizes newly synthesized proteins; determinant of replicative life span; involved in mitochondrial segregation
YBR186W	0.00427089	MSN4	YBR186W|PCH2|S000000390|Nucleolar component of the pachytene checkpoint, which prevents chromosome segregation when recombination and chromosome synapsis are defective; also represses meiotic interhomolog recombination in the rDNA
YLR255C	0.0037187	MSN4	YLR255C||S000004245|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJL211C	0.00370011	MSN4	YJL211C||S000003747|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YJL210W/PEX2
YOR056C	0.00346896	MSN4	YOR056C|NOB1|S000005582|Essential nuclear protein involved in proteasome maturation and synthesis of 40S ribosomal subunits; required for cleavage of the 20S pre-rRNA to generate the mature 18S rRNA
YKL187C	0.00302799	MSN4	YKL187C||S000001670|Putative protein of unknown function; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies
YOR256C	0.0023803	MSN4	YOR256C|TRE2|S000005782|Protein that functions with Tre1p to regulate ubiquitylation and vacuolar degradation of the metal transporter Smf1p; has similarity to transferrin receptors; inviability of null mutant in systematic studies is due to proximity to CDC31
YNL294C	0.00192332	MSN4	YNL294C|RIM21|S000005238|Component of the RIM101 pathway, has a role in cell wall construction and alkaline pH response; has similarity to A. nidulans PalH
YKL059C	0.00163344	MSN4	YKL059C|MPE1|S000001542|Essential conserved subunit of CPF (cleavage and polyadenylation factor), plays a role in 3' end formation of mRNA via the specific cleavage and polyadenylation of pre-mRNA, contains a putative RNA-binding zinc knuckle motif
YGR178C	0.00155739	MSN4	YGR178C|PBP1|S000003410|Protein interacting with poly(A)-binding protein Pab1p; likely involved in controlling the extent of mRNA polyadenylation; forms a complex with Mkt1p that may regulate HO translation; interacts with Lsm12p in a copurification assay
YLR263W	0.00053929	MSN4	YLR263W|RED1|S000004253|Protein component of the axial elements of the synaptonemal complex, involved in chromosome segregation during the first meiotic division; interacts with Hop1p; required for wild-type levels of Mek1p kinase activity
