YJR005C-A	2.00438	RPN4	YJR005C-A||S000028523|Putative protein of unknown function, originally identified as a syntenic homolog of an Ashbya gossypii gene
YJL115W	1.85087	RPN4	YJL115W|ASF1|S000003651|Nucleosome assembly factor, involved in chromatin assembly and disassembly, anti-silencing protein that causes derepression of silent loci when overexpressed; plays a role in regulating Ty1 transposition
YBL085W	1.70665	RPN4	YBL085W|BOI1|S000000181|Protein implicated in polar growth, functionally redundant with Boi2p; interacts with bud-emergence protein Bem1p; contains an SH3 (src homology 3) domain and a PH (pleckstrin homology) domain
YJR094C	1.50543	RPN4	YJR094C|IME1|S000003854|Master regulator of meiosis that is active only during meiotic events, activates transcription of early meiotic genes through interaction with Ume6p, degraded by the 26S proteasome following phosphorylation by Ime2p
YGL035C	1.43969	RPN4	YGL035C|MIG1|S000003003|Transcription factor involved in glucose repression; sequence specific DNA binding protein containing two Cys2His2 zinc finger motifs; regulated by the SNF1 kinase and the GLC7 phosphatase
YJL116C	1.43456	RPN4	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
YKL218C	1.32338	RPN4	YKL218C|SRY1|S000001701|3-hydroxyaspartate dehydratase, deaminates L-threo-3-hydroxyaspartate to form oxaloacetate and ammonia; required for survival in the presence of hydroxyaspartate
YDR510W	1.0599	RPN4	YDR510W|SMT3|S000002918|Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics
YOL123W	1.0211	RPN4	YOL123W|HRP1|S000005483|Subunit of cleavage factor I, a five-subunit complex required for the cleavage and polyadenylation of pre-mRNA 3' ends; RRM-containing heteronuclear RNA binding protein and hnRNPA/B family member that binds to poly (A) signal sequences
YOR052C	1.01968	RPN4	YOR052C||S000005578|Nuclear protein of unknown function; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner and by weak acid
YLL045C	0.912969	RPN4	YLL045C|RPL8B|S000003968|Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits
YDL037C	0.911759	RPN4	YDL037C|BSC1|S000002195|Protein of unconfirmed function, similar to cell surface flocculin Muc1p; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YGR286C	0.911267	RPN4	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
YNL251C	0.906565	RPN4	YNL251C|NRD1|S000005195|RNA-binding protein that interacts with the C-terminal domain of the RNA polymerase II large subunit (Rpo21p), required for transcription termination and 3' end maturation of nonpolyadenylated RNAs
YBR114W	0.87671	RPN4	YBR114W|RAD16|S000000318|Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad7p) during nucleotide excision repair; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex
YAL003W	0.857586	RPN4	YAL003W|EFB1|S000000003|Translation elongation factor 1 beta; stimulates nucleotide exchange to regenerate EF-1 alpha-GTP for the next elongation cycle; part of the EF-1 complex, which facilitates binding of aminoacyl-tRNA to the ribosomal A site
YJL107C	0.853531	RPN4	YJL107C||S000003643|Putative protein of unknown function; expression is induced by activation of the HOG1 mitogen-activated signaling pathway and this induction is Hog1p/Pbs2p dependent; YJL107C and adjacent ORF, YJL108C are merged in related fungi
YGL103W	0.839011	RPN4	YGL103W|RPL28|S000003071|Ribosomal protein of the large (60S) ribosomal subunit, has similarity to E. coli L15 and rat L27a ribosomal proteins; may have peptidyl transferase activity; can mutate to cycloheximide resistance
YMR100W	0.818663	RPN4	YMR100W|MUB1|S000004706|Protein of unknown function, deletion causes multi-budding phenotype; has similarity to Aspergillus nidulans samB gene
YER177W	0.797768	RPN4	YER177W|BMH1|S000000979|14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling
YMR102C	0.794498	RPN4	YMR102C||S000004708|Protein of unknown function; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance; mutant shows increased resistance to azoles; YMR102C is not an essential gene
YDR224C	0.785303	RPN4	YDR224C|HTB1|S000002632|One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation
YFL023W	0.746425	RPN4	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
YBR112C	0.729128	RPN4	YBR112C|CYC8|S000000316|General transcriptional co-repressor, acts together with Tup1p; also acts as part of a transcriptional co-activator complex that recruits the SWI/SNF and SAGA complexes to promoters
YJR094W-A	0.725393	RPN4	YJR094W-A|RPL43B|S000003855|Protein component of the large (60S) ribosomal subunit, identical to Rpl43Ap and has similarity to rat L37a ribosomal protein
YGR255C	0.697207	RPN4	YGR255C|COQ6|S000003487|Putative flavin-dependent monooxygenase, 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
YBR184W	0.694766	RPN4	YBR184W||S000000388|Putative protein of unknown function; YBR184W is not an essential gene
YFR056C	0.661321	RPN4	YFR056C||S000001951|Dubious open reading frame unlikely to encode a protein based on available experimental and comparative sequence data; partially overlaps the uncharacterized gene YFR055W
YGR060W	0.658157	RPN4	YGR060W|ERG25|S000003292|C-4 methyl sterol oxidase, catalyzes the first of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; mutants accumulate the sterol intermediate 4,4-dimethylzymosterol
YKL216W	0.655643	RPN4	YKL216W|URA1|S000001699|Dihydroorotate dehydrogenase, catalyzes the fourth enzymatic step in the de novo biosynthesis of pyrimidines, converting dihydroorotic acid into orotic acid
YBR208C	0.620565	RPN4	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
YLR260W	0.610561	RPN4	YLR260W|LCB5|S000004250|Minor sphingoid long-chain base kinase, paralog of Lcb4p responsible for few percent of the total activity, possibly involved in synthesis of long-chain base phosphates, which function as signaling molecules
YLR448W	0.60128	RPN4	YLR448W|RPL6B|S000004440|Protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Ap and to rat L6 ribosomal protein; binds to 5.8S rRNA
YIL031W	0.588964	RPN4	YIL031W|ULP2|S000001293|Peptidase that deconjugates Smt3/SUMO-1 peptides from proteins, plays a role in chromosome cohesion at centromeric regions and recovery from checkpoint arrest induced by DNA damage or DNA replication defects; potential Cdc28p substrate
YHR021C	0.575131	RPN4	YHR021C|RPS27B|S000001063|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps27Ap and has similarity to rat S27 ribosomal protein
YGR048W	0.573315	RPN4	YGR048W|UFD1|S000003280|Protein that interacts with Cdc48p and Npl4p, involved in recognition of polyubiquitinated proteins and their presentation to the 26S proteasome for degradation; involved in transporting proteins from the ER to the cytosol
YML007W	0.564456	RPN4	YML007W|YAP1|S000004466|Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium
YDR414C	0.560058	RPN4	YDR414C|ERD1|S000002822|Predicted membrane protein required for the retention of lumenal endoplasmic reticulum proteins; mutants secrete the endogenous ER protein, BiP (Kar2p)
YGR140W	0.54195	RPN4	YGR140W|CBF2|S000003372|Essential kinetochore protein, component of the CBF3 multisubunit complex that binds to the CDEIII region of the centromere; Cbf2p also binds to the CDEII region possibly forming a different multimeric complex, ubiquitinated in vivo
YJL090C	0.53298	RPN4	YJL090C|DPB11|S000003626|Subunit of DNA Polymerase II Epsilon complex; has BRCT domain, required on the prereplicative complex at replication origins for loading DNA polymerases to initiate DNA synthesis, also required for S/M checkpoint control
YOL038W	0.530233	RPN4	YOL038W|PRE6|S000005398|Alpha 4 subunit of the 20S proteasome; may replace alpha 3 subunit (Pre9p) under stress conditions to create a more active proteasomal isoform; GFP-fusion protein relocates from cytosol to the mitochondrial surface upon oxidative stress
YNL323W	0.527803	RPN4	YNL323W|LEM3|S000005267|Membrane protein of the plasma membrane and ER, involved in translocation of phospholipids and alkylphosphocholine drugs across the plasma membrane
YFR055W	0.515314	RPN4	YFR055W|IRC7|S000001952|Putative cystathionine beta-lyase; involved in copper ion homeostasis and sulfur metabolism; null mutant displays increased levels of spontaneous Rad52p foci; expression induced by nitrogen limitation in a GLN3, GAT1-dependent manner
YIL142C-A	0.514502	RPN4	YIL142C-A||S000028796|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL211C	0.497665	RPN4	YDL211C||S000002370|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole
YKL190W	0.496737	RPN4	YKL190W|CNB1|S000001673|Calcineurin B; the regulatory subunit of calcineurin, a Ca++/calmodulin-regulated type 2B protein phosphatase which regulates Crz1p (a stress-response transcription factor), the other calcineurin subunit is encoded by CNA1 and/or CMP1
YFL022C	0.490835	RPN4	YFL022C|FRS2|S000001872|Alpha subunit of cytoplasmic phenylalanyl-tRNA synthetase, forms a tetramer with Frs1p to form active enzyme; evolutionarily distant from mitochondrial phenylalanyl-tRNA synthetase based on protein sequence, but substrate binding is similar
YNR051C	0.486743	RPN4	YNR051C|BRE5|S000005334|Ubiquitin protease cofactor, forms deubiquitination complex with Ubp3p that coregulates anterograde and retrograde transport between the endoplasmic reticulum and Golgi compartments; null is sensitive to brefeldin A
YML032C	0.485713	RPN4	YML032C|RAD52|S000004494|Protein that stimulates strand exchange by facilitating Rad51p binding to single-stranded DNA; anneals complementary single-stranded DNA; involved in the repair of double-strand breaks in DNA during vegetative growth and meiosis
YBR106W	0.483125	RPN4	YBR106W|PHO88|S000000310|Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations
YDL070W	0.474122	RPN4	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
YMR101C	0.473166	RPN4	YMR101C|SRT1|S000004707|Cis-prenyltransferase involved in synthesis of long-chain dolichols (19-22 isoprene units; as opposed to Rer2p which synthesizes shorter-chain dolichols); localizes to lipid bodies; transcription is induced during stationary phase
YLL027W	0.472814	RPN4	YLL027W|ISA1|S000003950|Mitochondrial matrix protein involved in biogenesis of the iron-sulfur (Fe/S) cluster of Fe/S proteins, isa1 deletion causes loss of mitochondrial DNA and respiratory deficiency; depletion reduces growth on nonfermentable carbon sources
YHL024W	0.472555	RPN4	YHL024W|RIM4|S000001016|Putative RNA-binding protein required for the expression of early and middle sporulation genes
YAL005C	0.465692	RPN4	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
YML088W	0.463934	RPN4	YML088W|UFO1|S000004553|F-box receptor protein, subunit of the Skp1-Cdc53-F-box receptor (SCF) E3 ubiquitin ligase complex; binds to phosphorylated Ho endonuclease, allowing its ubiquitylation by SCF and subsequent degradation
YAL053W	0.461699	RPN4	YAL053W|FLC2|S000000049|Putative FAD transporter; required for uptake of FAD into endoplasmic reticulum; involved in cell wall maintenance
YPL110C	0.460245	RPN4	YPL110C|GDE1|S000006031|Glycerophosphocholine (GroPCho) phosphodiesterase; hydrolyzes GroPCho to choline and glycerolphosphate, for use as a phosphate source and as a precursor for phosphocholine synthesis; may interact with ribosomes
YOR355W	0.45824	RPN4	YOR355W|GDS1|S000005882|Protein of unknown function, required for growth on glycerol as a carbon source; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER012W	0.455113	RPN4	YER012W|PRE1|S000000814|Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle
YKL118W	0.447712	RPN4	YKL118W||S000001601|Dubious open reading frame, unlikely to encode a protein; partially overlaps the verified gene VPH2
YPL177C	0.442832	RPN4	YPL177C|CUP9|S000006098|Homeodomain-containing transcriptional repressor of PTR2, which encodes a major peptide transporter; imported peptides activate ubiquitin-dependent proteolysis, resulting in degradation of Cup9p and de-repression of PTR2 transcription
YJR006W	0.442684	RPN4	YJR006W|POL31|S000003766|DNA polymerase III (delta) subunit, essential for cell viability; involved in DNA replication and DNA repair
YKL054C	0.435018	RPN4	YKL054C|DEF1|S000001537|RNAPII degradation factor, forms a complex with Rad26p in chromatin, enables ubiquitination and proteolysis of RNAPII present in an elongation complex; mutant is deficient in Zip1p loading onto chromosomes during meiosis
YOR226C	0.434522	RPN4	YOR226C|ISU2|S000005752|Conserved protein of the mitochondrial matrix, required for synthesis of mitochondrial and cytosolic iron-sulfur proteins, performs a scaffolding function in mitochondria during Fe/S cluster assembly; isu1 isu2 double mutant is inviable
YGR138C	0.432106	RPN4	YGR138C|TPO2|S000003370|Polyamine transport protein specific for spermine; localizes to the plasma membrane; transcription of TPO2 is regulated by Haa1p; member of the major facilitator superfamily
YCL058C	0.427692	RPN4	YCL058C|FYV5|S000000563|Protein of unknown function, required for survival upon exposure to K1 killer toxin; involved in ion homeostasis
YIL142W	0.425622	RPN4	YIL142W|CCT2|S000001404|Subunit beta of the cytosolic chaperonin Cct ring complex, related to Tcp1p, required for the assembly of actin and tubulins in vivo
YKL110C	0.423657	RPN4	YKL110C|KTI12|S000001593|Protein that plays a role, with Elongator complex, in modification of wobble nucleosides in tRNA; involved in sensitivity to G1 arrest induced by zymocin; interacts with chromatin throughout the genome; also interacts with Cdc19p
YHR006W	0.423302	RPN4	YHR006W|STP2|S000001048|Transcription factor, activated by proteolytic processing in response to signals from the SPS sensor system for external amino acids; activates transcription of amino acid permease genes
YDL246C	0.41703	RPN4	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
YEL037C	0.412996	RPN4	YEL037C|RAD23|S000000763|Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins
YOL086W-A	0.406488	RPN4	YOL086W-A||S000007626|Putative protein of unknown function; identified by homology
YAL035W	0.405601	RPN4	YAL035W|FUN12|S000000033|GTPase, required for general translation initiation by promoting Met-tRNAiMet binding to ribosomes and ribosomal subunit joining; homolog of bacterial IF2
YIL072W	0.400014	RPN4	YIL072W|HOP1|S000001334|Meiosis-specific DNA binding protein that displays Red1p dependent localization to the unsynapsed axial-lateral elements of the synaptonemal complex; required for homologous chromosome synapsis and chiasma formation
YGR051C	0.394593	RPN4	YGR051C||S000003283|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YGR051C is not an essential gene
YDR043C	0.392895	RPN4	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
YCR061W	0.392699	RPN4	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
YJL106W	0.392248	RPN4	YJL106W|IME2|S000003642|Serine/threonine protein kinase involved in activation of meiosis, associates with Ime1p and mediates its stability, activates Ndt80p; IME2 expression is positively regulated by Ime1p
YGR052W	0.391421	RPN4	YGR052W|FMP48|S000003284|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; induced by treatment with 8-methoxypsoralen and UVA irradiation
YEL033W	0.390499	RPN4	YEL033W|MTC7|S000000759|Predicted metabolic role based on network analysis derived from ChIP experiments, a large-scale deletion study and localization of transcription factor binding sites; null mutant is sensitive to temperature oscillation in a cdc13-1 mutant
YHR183W	0.387965	RPN4	YHR183W|GND1|S000001226|6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone and adaptation to oxidative stress
YHL031C	0.387405	RPN4	YHL031C|GOS1|S000001023|v-SNARE protein involved in Golgi transport, homolog of the mammalian protein GOS-28/GS28
YKR092C	0.383535	RPN4	YKR092C|SRP40|S000001800|Nucleolar, serine-rich protein with a role in preribosome assembly or transport; may function as a chaperone of small nucleolar ribonucleoprotein particles (snoRNPs); immunologically and structurally to rat Nopp140
YER064C	0.383156	RPN4	YER064C||S000000866|Non-essential nuclear protein; null mutation has global effects on transcription
YGL122C	0.382988	RPN4	YGL122C|NAB2|S000003090|Nuclear polyadenylated RNA-binding protein; autoregulates mRNA levels; related to human hnRNPs; has nuclear localization signal sequence that binds to Kap104p; required for poly(A) tail length control and nuclear mRNA export
YBR171W	0.380064	RPN4	YBR171W|SEC66|S000000375|Non-essential subunit of Sec63 complex (Sec63p, Sec62p, Sec66p and Sec72p); with Sec61 complex, Kar2p/BiP and Lhs1p forms a channel competent for SRP-dependent and post-translational SRP-independent protein targeting and import into the ER
YOR362C	0.374629	RPN4	YOR362C|PRE10|S000005889|Alpha 7 subunit of the 20S proteasome
YBR174C	0.373137	RPN4	YBR174C||S000000378|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF YBR175W; null mutant is viable and sporulation defective
YBR009C	0.370905	RPN4	YBR009C|HHF1|S000000213|One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity
YNL027W	0.365677	RPN4	YNL027W|CRZ1|S000004972|Transcription factor that activates transcription of genes involved in stress response; nuclear localization is positively regulated by calcineurin-mediated dephosphorylation
YBR113W	0.365596	RPN4	YBR113W||S000000317|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CYC8
YLR287C-A	0.363815	RPN4	YLR287C-A|RPS30A|S000004278|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps30Bp and has similarity to rat S30 ribosomal protein
YOR062C	0.363382	RPN4	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
YDL007W	0.357199	RPN4	YDL007W|RPT2|S000002165|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for normal peptide hydrolysis by the core 20S particle
YDR073W	0.355144	RPN4	YDR073W|SNF11|S000002480|Subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; interacts with a highly conserved 40-residue sequence of Snf2p
YCR081C-A	0.354618	RPN4	YCR081C-A||S000028609|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps with SRB8/YCR081W; identified by gene-trapping, microarray expression analysis, and genome-wide homology searching
YML125C	0.353861	RPN4	YML125C|PGA3|S000004594|Essential protein required for maturation of Gas1p and Pho8p, proposed to be involved in protein trafficking; GFP-fusion protein localizes to the endoplasmic reticulum; null mutants have a cell separation defect
YDL193W	0.352077	RPN4	YDL193W|NUS1|S000002352|Prenyltransferase, required for cell viability; involved in protein trafficking
YGR047C	0.352052	RPN4	YGR047C|TFC4|S000003279|One of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauA domain of TFIIIC that binds BoxA DNA promoter sites of tRNA and similar genes; has TPR motifs; human homolog is TFIIIC-102
YKR011C	0.350558	RPN4	YKR011C||S000001719|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus
YJL036W	0.350016	RPN4	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
YPR008W	0.347178	RPN4	YPR008W|HAA1|S000006212|Transcriptional activator involved in the transcription of TPO2, HSP30 and other genes encoding membrane stress proteins; involved in adaptation to weak acid stress
YER095W	0.346527	RPN4	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
YML111W	0.346174	RPN4	YML111W|BUL2|S000004579|Component of the Rsp5p E3-ubiquitin ligase complex, involved in intracellular amino acid permease sorting, functions in heat shock element mediated gene expression, essential for growth in stress conditions, functional homolog of BUL1
YJL200C	0.345227	RPN4	YJL200C|ACO2|S000003736|Putative mitochondrial aconitase isozyme; similarity to Aco1p, an aconitase required for the TCA cycle; expression induced during growth on glucose, by amino acid starvation via Gcn4p, and repressed on ethanol
YOR157C	0.344416	RPN4	YOR157C|PUP1|S000005683|Endopeptidase with trypsin-like activity that cleaves after basic residues; beta 2 subunit of 20S proteasome, synthesized as a proprotein before being proteolytically processed for assembly into 20S particle; human homolog is subunit Z
YBL086C	0.344025	RPN4	YBL086C||S000000182|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YLL043W	0.34277	RPN4	YLL043W|FPS1|S000003966|Plasma membrane channel, member of major intrinsic protein (MIP) family; involved in efflux of glycerol and in uptake of acetic acid and the trivalent metalloids arsenite and antimonite; phosphorylated by Hog1p MAPK under acetate stress
YGL201C	0.34146	RPN4	YGL201C|MCM6|S000003169|Protein involved in DNA replication; component of the Mcm2-7 hexameric complex that binds chromatin as a part of the pre-replicative complex
YGL172W	0.341079	RPN4	YGL172W|NUP49|S000003140|Subunit of the Nsp1p-Nup57p-Nup49p-Nic96p subcomplex of the nuclear pore complex (NPC), required for nuclear export of ribosomes
YOR389W	0.336387	RPN4	YOR389W||S000005916|Putative protein of unknown function; expression regulated by copper levels
YHR182C-A	0.335639	RPN4	YHR182C-A||S000028784|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YFR003C	0.334653	RPN4	YFR003C|YPI1|S000001899|Inhibitor of the type I protein phosphatase Glc7p, which is involved in regulation of a variety of metabolic processes; overproduction causes decreased cellular content of glycogen
YGL033W	0.333424	RPN4	YGL033W|HOP2|S000003001|Meiosis-specific protein that localizes to chromosomes, preventing synapsis between nonhomologous chromosomes and ensuring synapsis between homologs; complexes with Mnd1p to promote homolog pairing and meiotic double-strand break repair
YML092C	0.333364	RPN4	YML092C|PRE8|S000004557|Alpha 2 subunit of the 20S proteasome
YDR431W	0.3299	RPN4	YDR431W||S000002839|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR374W-A	0.323339	RPN4	YDR374W-A||S000113553|Putative protein of unknown function
YJL007C	0.320563	RPN4	YJL007C||S000003544|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJR159W	0.320391	RPN4	YJR159W|SOR1|S000003920|Sorbitol dehydrogenase; expression is induced in the presence of sorbitol
YDL028C	0.317499	RPN4	YDL028C|MPS1|S000002186|Dual-specificity kinase required for spindle pole body (SPB) duplication and spindle checkpoint function; substrates include SPB proteins Spc42p, Spc110p, and Spc98p, mitotic exit network protein Mob1p, and checkpoint protein Mad1p
YOL087C	0.315788	RPN4	YOL087C||S000005447|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; deletion mutant is sensitive to various chemicals including phenanthroline, sanguinarine, and nordihydroguaiaretic acid
YDL145C	0.309908	RPN4	YDL145C|COP1|S000002304|Alpha subunit of COPI vesicle coatomer complex, which surrounds transport vesicles in the early secretory pathway
YKL117W	0.309746	RPN4	YKL117W|SBA1|S000001600|Co-chaperone that binds to and regulates Hsp90 family chaperones; important for pp60v-src activity in yeast; homologous to the mammalian p23 proteins and like p23 can regulate telomerase activity
YBL058W	0.309603	RPN4	YBL058W|SHP1|S000000154|UBX (ubiquitin regulatory X) domain-containing protein that regulates Glc7p phosphatase activity and interacts with Cdc48p; interacts with ubiquitylated proteins in vivo and is required for degradation of a ubiquitylated model substrate
YPR102C	0.308317	RPN4	YPR102C|RPL11A|S000006306|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl11Bp; involved in ribosomal assembly; depletion causes degradation of proteins and RNA of the 60S subunit; has similarity to E. coli L5 and rat L11
YOR050C	0.307563	RPN4	YOR050C||S000005576|Hypothetical protein
YMR067C	0.305897	RPN4	YMR067C|UBX4|S000004671|UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p
YLR096W	0.301528	RPN4	YLR096W|KIN2|S000004086|Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane; closely related to Kin1p
YML065W	0.300096	RPN4	YML065W|ORC1|S000004530|Largest subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; exhibits ATPase activity
YLR154W-A	0.299563	RPN4	YLR154W-A||S000028675|Dubious open reading frame unlikely to encode a protein; encoded within the the 25S rRNA gene on the opposite strand
YMR246W	0.28825	RPN4	YMR246W|FAA4|S000004860|Long chain fatty acyl-CoA synthetase, regulates protein modification during growth in the presence of ethanol, functions to incorporate palmitic acid into phospholipids and neutral lipids
YPR041W	0.286991	RPN4	YPR041W|TIF5|S000006245|Translation initiation factor eIF-5; N-terminal domain functions as a GTPase-activating protein to mediate hydrolysis of ribosome-bound GTP; C-terminal domain is the core of ribosomal preinitiation complex formation
YOR051C	0.286959	RPN4	YOR051C||S000005577|Nuclear protein that inhibits replication of Brome mosaic virus in S. cerevisiae, which is a model system for studying replication of positive-strand RNA viruses in their natural hosts
YML130C	0.28468	RPN4	YML130C|ERO1|S000004599|Thiol oxidase required for oxidative protein folding in the endoplasmic reticulum
YLR154W-B	0.282547	RPN4	YLR154W-B||S000028563|Dubious open reading frame unlikely to encode a protein; encoded within the the 25S rRNA gene on the opposite strand
YFL036W	0.281026	RPN4	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
YOL034W	0.280047	RPN4	YOL034W|SMC5|S000005394|Structural maintenance of chromosomes (SMC) protein; essential subunit of the Mms21-Smc5-Smc6 complex; required for growth and DNA repair; S. pombe homolog forms a heterodimer with S. pombe Rad18p that is involved in DNA repair
YKL015W	0.276302	RPN4	YKL015W|PUT3|S000001498|Transcriptional activator of proline utilization genes, constitutively binds PUT1 and PUT2 promoter sequences and undergoes a conformational change to form the active state; has a Zn(2)-Cys(6) binuclear cluster domain
YER075C	0.272441	RPN4	YER075C|PTP3|S000000877|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 cytoplasm
YOR146W	0.271384	RPN4	YOR146W||S000005672|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; open reading frame overlaps the verified gene PNO1/YOR145C
YDR363W-A	0.270388	RPN4	YDR363W-A|SEM1|S000007235|Component of the lid subcomplex of the regulatory subunit of the 26S proteasome; ortholog of human DSS1
YBL041W	0.270344	RPN4	YBL041W|PRE7|S000000137|Beta 6 subunit of the 20S proteasome
YCR082W	0.270174	RPN4	YCR082W|AHC2|S000000678|Protein of unknown function, putative transcriptional regulator; proposed to be a Ada Histone acetyltransferase complex component; GFP tagged protein is localized to the cytoplasm and nucleus
YDR285W	0.270132	RPN4	YDR285W|ZIP1|S000002693|Transverse filament protein of the synaptonemal complex; required for normal levels of meiotic recombination and pairing between homologous chromosome during meiosis; potential Cdc28p substrate
YER129W	0.268477	RPN4	YER129W|SAK1|S000000931|Upstream serine/threonine kinase for the SNF1 complex; partially redundant with Elm1p and Tos3p; members of this family have functional orthology with LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome
YBR300C	0.267575	RPN4	YBR300C||S000000504|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YBR301W; YBR300C is not an essential gene
YNL155W	0.267275	RPN4	YNL155W||S000005099|Putative protein of unknown function, contains DHHC domain, also predicted to have thiol-disulfide oxidoreductase active site
YBR010W	0.266765	RPN4	YBR010W|HHT1|S000000214|One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation
YHR021W-A	0.266662	RPN4	YHR021W-A|ECM12|S000003531|Non-essential protein of unknown function
YEL056W	0.265281	RPN4	YEL056W|HAT2|S000000782|Subunit of the Hat1p-Hat2p histone acetyltransferase complex; required for high affinity binding of the complex to free histone H4, thereby enhancing Hat1p activity; similar to human RbAp46 and 48; has a role in telomeric silencing
YNL172W	0.263735	RPN4	YNL172W|APC1|S000005116|Largest subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition
YMR281W	0.262615	RPN4	YMR281W|GPI12|S000004894|ER membrane protein involved in the second step of glycosylphosphatidylinositol (GPI) anchor assembly, the de-N-acetylation of the N-acetylglucosaminylphosphatidylinositol intermediate; functional homolog of human PIG-Lp
YCL024W	0.262158	RPN4	YCL024W|KCC4|S000000529|Protein kinase of the bud neck involved in the septin checkpoint, associates with septin proteins, negatively regulates Swe1p by phosphorylation, shows structural homology to bud neck kinases Gin4p and Hsl1p
YEL032W	0.26201	RPN4	YEL032W|MCM3|S000000758|Protein involved in DNA replication; component of the Mcm2-7 hexameric complex that binds chromatin as a part of the pre-replicative complex
YIL126W	0.261234	RPN4	YIL126W|STH1|S000001388|ATPase component of the RSC chromatin remodeling complex; required for expression of early meiotic genes; essential helicase-related protein homologous to Snf2p
YGL011C	0.259668	RPN4	YGL011C|SCL1|S000002979|Alpha 1 subunit of the 20S core complex of the 26S proteasome involved in the degradation of ubiquitinated substrates; essential for growth; detected in the mitochondria
YHR027C	0.259212	RPN4	YHR027C|RPN1|S000001069|Non-ATPase base subunit of the 19S regulatory particle of the 26S proteasome; may participate in the recognition of several ligands of the proteasome; contains a leucine-rich repeat (LRR) domain, a site for protein?protein interactions
YNL313C	0.259007	RPN4	YNL313C||S000005257|Putative protein of unknown function; identified as interacting with Kar2p, Grs1p, and Tub3p in high-throughput TAP-tagging experiments; YNL313C is an essential gene
YJL014W	0.258866	RPN4	YJL014W|CCT3|S000003551|Subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p, required for the assembly of actin and tubulins in vivo
YNL304W	0.258027	RPN4	YNL304W|YPT11|S000005248|Rab-type small GTPase that interacts with the C-terminal tail domain of Myo2p to mediate distribution of mitochondria to daughter cells
YPR185W	0.25771	RPN4	YPR185W|ATG13|S000006389|Regulatory subunit of the Atg1p signaling complex; stimulates Atg1p kinase activity; required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; involved in Atg9p, Atg23p, and Atg27p cycling
YPL058C	0.257034	RPN4	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
YOR145C	0.256566	RPN4	YOR145C|PNO1|S000005671|Essential nucleolar protein required for pre-18S rRNA processing, interacts with Dim1p, an 18S rRNA dimethyltransferase, and also with Nob1p, which is involved in proteasome biogenesis; contains a KH domain
YJL105W	0.255121	RPN4	YJL105W|SET4|S000003641|Protein of unknown function, contains a SET domain
YJL008C	0.254467	RPN4	YJL008C|CCT8|S000003545|Subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p, required for the assembly of actin and tubulins in vivo
YOR359W	0.25224	RPN4	YOR359W|VTS1|S000005886|Post-transcriptional gene regulator, RNA-binding protein containing a SAM domain; shows genetic interactions with Vti1p, which is a v-SNARE involved in cis-Golgi membrane traffic
YBR202W	0.250212	RPN4	YBR202W|MCM7|S000000406|Component of the hexameric MCM complex, which is important for priming origins of DNA replication in G1 and becomes an active ATP-dependent helicase that promotes DNA melting and elongation when activated by Cdc7p-Dbf4p in S-phase
YER054C	0.250021	RPN4	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
YJL015C	0.249641	RPN4	YJL015C||S000003552|Dubious open reading frame unlikely to encode a functional protein; expression if heat-inducible; located in promoter region of essential CCT3 gene encoding a subunit of the cytosolic chaperonin Cct ring complex, overlaps ORF YJL016W
YFR051C	0.248295	RPN4	YFR051C|RET2|S000001947|Delta subunit of the coatomer complex (COPI), which coats Golgi-derived transport vesicles; involved in retrograde transport between Golgi and ER
YPR065W	0.24656	RPN4	YPR065W|ROX1|S000006269|Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity
YEL034C-A	0.240947	RPN4	YEL034C-A||S000028743|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; completely overlaps HYP2/YEL034W, a verified gene that encodes eiF-5A
YLR154W-C	0.239589	RPN4	YLR154W-C|TAR1|S000028422|Mitochondrial protein of unknown function, overexpression suppresses an rpo41 mutation affecting mitochondrial RNA polymerase; encoded within the 25S rRNA gene on the opposite strand
YOL086C	0.239114	RPN4	YOL086C|ADH1|S000005446|Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway
YOL159C-A	0.237499	RPN4	YOL159C-A||S000007627|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YFL015W-A	0.237395	RPN4	YFL015W-A||S000028765|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR097W	0.236992	RPN4	YGR097W|ASK10|S000003329|Component of the RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress; has a role in destruction of Ssn8p, which relieves repression of stress-response genes
YDR270W	0.236808	RPN4	YDR270W|CCC2|S000002678|Cu(+2)-transporting P-type ATPase, required for export of copper from the cytosol into an extracytosolic compartment; has similarity to human proteins involved in Menkes and Wilsons diseases
YPL108W	0.235273	RPN4	YPL108W||S000006029|Cytoplasmic protein of unknown function; non-essential gene that is induced in a GDH1 deleted strain with altered redox metabolism; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YHR203C	0.234077	RPN4	YHR203C|RPS4B|S000001246|Protein component of the small (40S) ribosomal subunit; identical to Rps4Ap and has similarity to rat S4 ribosomal protein
YGL148W	0.233874	RPN4	YGL148W|ARO2|S000003116|Bifunctional chorismate synthase and flavin reductase, catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to form chorismate, which is a precursor to aromatic amino acids
YPL205C	0.233285	RPN4	YPL205C||S000006126|Hypothetical protein; deletion of locus affects telomere length
YBR060C	0.231639	RPN4	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
YPL204W	0.231478	RPN4	YPL204W|HRR25|S000006125|Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)
YBR049C	0.23126	RPN4	YBR049C|REB1|S000000253|RNA polymerase I enhancer binding protein; DNA binding protein which binds to genes transcribed by both RNA polymerase I and RNA polymerase II; required for termination of RNA polymerase I transcription
YOR315W	0.230844	RPN4	YOR315W|SFG1|S000005842|Nuclear protein, putative transcription factor required for growth of superficial pseudohyphae (which do not invade the agar substrate) but not for invasive pseudohyphal growth; may act together with Phd1p; potential Cdc28p substrate
YIR007W	0.229875	RPN4	YIR007W||S000001446|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YIR007W is a non-essential gene
YHR154W	0.229228	RPN4	YHR154W|RTT107|S000001197|Protein implicated in Mms22-dependent DNA repair during S phase, DNA damage induces phosphorylation by Mec1p at one or more SQ/TQ motifs; interacts with Mms22p and Slx4p; has four BRCT domains; has a role in regulation of Ty1 transposition
YDR279W	0.228565	RPN4	YDR279W|RNH202|S000002687|Ribonuclease H2 subunit, required for RNase H2 activity
YGR146C-A	0.228066	RPN4	YGR146C-A||S000028638|Putative protein of unknown function
YML031C-A	0.225377	RPN4	YML031C-A||S000028809|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF NDC1/YML031W; questionable ORF from MIPS
YIL164C	0.224424	RPN4	YIL164C|NIT1|S000001426|Nitrilase, member of the nitrilase branch of the nitrilase superfamily; in closely related species and other S. cerevisiae strain backgrounds YIL164C and adjacent ORF, YIL165C, likely constitute a single ORF encoding a nitrilase gene
YPR125W	0.22387	RPN4	YPR125W|YLH47|S000006329|Mitochondrial inner membrane protein exposed to the mitochondrial matrix, associates with mitochondrial ribosomes, NOT required for respiratory growth; homolog of human Letm1, a protein implicated in Wolf-Hirschhorn syndrome
YNR054C	0.222524	RPN4	YNR054C|ESF2|S000005337|Essential nucleolar protein involved in pre-18S rRNA processing; binds to RNA and stimulates ATPase activity of Dbp8; involved in assembly of the small subunit (SSU) processome
YDL143W	0.2222	RPN4	YDL143W|CCT4|S000002302|Subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p, required for the assembly of actin and tubulins in vivo
YMR108W	0.220813	RPN4	YMR108W|ILV2|S000004714|Acetolactate synthase, catalyses the first common step in isoleucine and valine biosynthesis and is the target of several classes of inhibitors, localizes to the mitochondria; expression of the gene is under general amino acid control
YMR244C-A	0.220349	RPN4	YMR244C-A||S000004857|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and nucleus and is induced in response to the DNA-damaging agent MMS; YMR244C-A is not an essential gene
YFR037C	0.217824	RPN4	YFR037C|RSC8|S000001933|Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters
YPL128C	0.217608	RPN4	YPL128C|TBF1|S000006049|Telobox-containing general regulatory factor; binds to TTAGGG repeats within subtelomeric anti-silencing regions (STARs) and possibly throughout the genome and mediates their insulating capacity by blocking silent chromatin propagation
YBR173C	0.216528	RPN4	YBR173C|UMP1|S000000377|Short-lived chaperone required for correct maturation of the 20S proteasome; may inhibit premature dimerization of proteasome half-mers; degraded by proteasome upon completion of its assembly
YLR407W	0.216493	RPN4	YLR407W||S000004399|Putative protein of unknown function; YLR407W is not an essential gene
YER167W	0.21547	RPN4	YER167W|BCK2|S000000969|Protein rich in serine and threonine residues involved in protein kinase C signaling pathway, which controls cell integrity; overproduction suppresses pkc1 mutations
YKR075C	0.214507	RPN4	YKR075C||S000001783|Protein of unknown function; similar to YOR062Cp and Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YDR122W	0.21352	RPN4	YDR122W|KIN1|S000002529|Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane; closely related to Kin2p
YBR284W	0.213439	RPN4	YBR284W||S000000488|Putative protein of unknown function; YBR284W is not an essential gene; null mutant exhibits decreased resistance to rapamycin and wortmannin
YNR013C	0.210613	RPN4	YNR013C|PHO91|S000005296|Low-affinity phosphate transporter of the vacuolar membrane; deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth
YPR029C	0.209066	RPN4	YPR029C|APL4|S000006233|Gamma-adaptin, large subunit of the clathrin-associated protein (AP-1) complex; binds clathrin; involved in vesicle mediated transport
YLR236C	0.208979	RPN4	YLR236C||S000004226|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCL023C	0.208697	RPN4	YCL023C||S000000528|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified ORF KCC4
YER113C	0.206092	RPN4	YER113C|TMN3|S000000915|Protein with a role in cellular adhesion and filamentous growth; similar to Emp70p and Tmn2p; member of Transmembrane Nine family with 9 transmembrane segments; localizes to Golgi; induced by 8-methoxypsoralen plus UVA irradiation
YDR346C	0.204037	RPN4	YDR346C|SVF1|S000002754|Protein with a potential role in cell survival pathways, required for the diauxic growth shift; expression in mammalian cells increases survival under conditions inducing apoptosis
YOL097W-A	0.201277	RPN4	YOL097W-A||S000028854|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YOR260W	0.200498	RPN4	YOR260W|GCD1|S000005786|Gamma subunit of the translation initiation factor eIF2B, the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a negative regulator of GCN4 expression
YMR070W	0.198773	RPN4	YMR070W|MOT3|S000004674|Nuclear transcription factor with two Cys2-His2 zinc fingers; involved in repression of a subset of hypoxic genes by Rox1p, repression of several DAN/TIR genes during aerobic growth, and repression of ergosterol biosynthetic genes
YKL201C	0.197901	RPN4	YKL201C|MNN4|S000001684|Putative positive regulator of mannosylphosphate transferase (Mnn6p), involved in mannosylphosphorylation of N-linked oligosaccharides; expression increases in late-logarithmic and stationary growth phases
YDL099W	0.197331	RPN4	YDL099W|BUG1|S000002257|Cis-golgi localized protein involved in ER to Golgi transport; forms a complex with the mammalian GRASP65 homolog, Grh1p; mutants are compromised for the fusion of ER-derived vesicles with Golgi membranes
YHL020C	0.1966	RPN4	YHL020C|OPI1|S000001012|Transcriptional regulator of a variety of genes; phosphorylation by protein kinase A stimulates Opi1p function in negative regulation of phospholipid biosynthetic genes; involved in telomere maintenance
YGL113W	0.195815	RPN4	YGL113W|SLD3|S000003081|Protein involved in the initiation of DNA replication, required for proper assembly of replication proteins at the origins of replication; interacts with Cdc45p
YMR076C	0.195627	RPN4	YMR076C|PDS5|S000004681|Protein required for establishment and maintenance of sister chromatid condensation and cohesion, colocalizes with cohesin on chromosomes in an interdependent manner, may function as a protein-protein interaction scaffold
YGR050C	0.194927	RPN4	YGR050C||S000003282|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJR137C	0.194223	RPN4	YJR137C|ECM17|S000003898|Sulfite reductase beta subunit, involved in amino acid biosynthesis, transcription repressed by methionine
YKL166C	0.192022	RPN4	YKL166C|TPK3|S000001649|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 Tpk2p
YOR072W-B	0.190882	RPN4	YOR072W-B||S000028516|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YER145C	0.189194	RPN4	YER145C|FTR1|S000000947|High affinity iron permease involved in the transport of iron across the plasma membrane; forms complex with Fet3p; expression is regulated by iron
YOR116C	0.188438	RPN4	YOR116C|RPO31|S000005642|RNA polymerase III subunit C160, part of core enzyme; similar to bacterial beta-prime subunit
YLR388W	0.188327	RPN4	YLR388W|RPS29A|S000004380|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps29Bp and has similarity to rat S29 and E. coli S14 ribosomal proteins
YKR102W	0.184358	RPN4	YKR102W|FLO10|S000001810|Lectin-like protein with similarity to Flo1p, thought to be involved in flocculation
YDR156W	0.183507	RPN4	YDR156W|RPA14|S000002563|RNA polymerase I subunit A14
YNL325C	0.182868	RPN4	YNL325C|FIG4|S000005269|Polyphosphatidylinositol phosphatase involved in the metabolism of phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2); required for efficient mating; physically associates with and regulated by Vac14p; contains a SAC1-like domain
YGL149W	0.181752	RPN4	YGL149W||S000003117|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF INO80/YGL150C.
YBR175W	0.181061	RPN4	YBR175W|SWD3|S000000379|Essential 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 and ortholog of mammalian WDR5
YFR039C	0.177153	RPN4	YFR039C||S000001935|Putative protein of unknown function; may be involved in response to high salt and changes in carbon source
YEL060C	0.176997	RPN4	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
YOR092W	0.176785	RPN4	YOR092W|ECM3|S000005618|Non-essential protein of unknown function; involved in signal transduction and the genotoxic response; induced rapidly in response to treatment with 8-methoxypsoralen and UVA irradiation
YER062C	0.173162	RPN4	YER062C|HOR2|S000000864|One of two redundant DL-glycerol-3-phosphatases (RHR2/GPP1 encodes the other) involved in glycerol biosynthesis; induced in response to hyperosmotic stress and oxidative stress, and during the diauxic transition
YAL036C	0.172721	RPN4	YAL036C|RBG1|S000000034|Member of the DRG family of GTP-binding proteins; interacts with translating ribosomes and with Tma46p
YFR004W	0.171694	RPN4	YFR004W|RPN11|S000001900|Metalloprotease subunit of the 19S regulatory particle of the 26S proteasome lid; couples the deubiquitination and degradation of proteasome substrates
YHL002W	0.169821	RPN4	YHL002W|HSE1|S000000994|Subunit of the endosomal Vps27p-Hse1p complex required for sorting of ubiquitinated membrane proteins into intralumenal vesicles prior to vacuolar degradation, as well as for recycling of Golgi proteins and formation of lumenal membranes
YLL004W	0.169811	RPN4	YLL004W|ORC3|S000003927|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing
YDR269C	0.169706	RPN4	YDR269C||S000002677|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YEL059C-A	0.169341	RPN4	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
YOL021C	0.168618	RPN4	YOL021C|DIS3|S000005381|Catalytic component of the exosome, involved in RNA processing and degradation; binds Gsp1p/Ran and enhances the GEF activity of Srm1p; implicated in mitotic control; homologous to the E. coli RNase R of the RNase II family
YFL015C	0.16715	RPN4	YFL015C||S000001879|Dubious open reading frame unlikely to encode a protein; partially overlaps dubious ORF YFL015W-A; YFL015C is not an essential gene
YLR025W	0.167142	RPN4	YLR025W|SNF7|S000004015|One of four subunits of the endosomal sorting complex required for transport III (ESCRT-III); involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway; recruited from the cytoplasm to endosomal membranes
YGR265W	0.166309	RPN4	YGR265W||S000003497|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF MES1/YGR264C, which encodes methionyl-tRNA synthetase
YHR152W	0.164437	RPN4	YHR152W|SPO12|S000001195|Nucleolar protein of unknown function, positive regulator of mitotic exit; involved in regulating release of Cdc14p from the nucleolus in early anaphase, may play similar role in meiosis
YOR325W	0.163606	RPN4	YOR325W||S000005852|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified ORF FRT1
YIL127C	0.163281	RPN4	YIL127C||S000001389|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleolus
YGR054W	0.162207	RPN4	YGR054W||S000003286|Eukaryotic initiation factor (eIF) 2A; associates specifically with both 40S subunits and 80 S ribosomes, and interacts genetically with both eIF5b and eIF4E; homologous to mammalian eIF2A
YKR093W	0.161419	RPN4	YKR093W|PTR2|S000001801|Integral membrane peptide transporter, mediates transport of di- and tri-peptides; conserved protein that contains 12 transmembrane domains; PTR2 expression is regulated by the N-end rule pathway via repression by Cup9p
YJR076C	0.1612	RPN4	YJR076C|CDC11|S000003837|Component of the septin ring of the mother-bud neck that is required for cytokinesis; septins recruit proteins to the neck and can act as a barrier to diffusion at the membrane, and they comprise the 10nm filaments seen with EM
YKL062W	0.160664	RPN4	YKL062W|MSN4|S000001545|Transcriptional activator related to Msn2p; activated in stress conditions, which results in translocation from the cytoplasm to the nucleus; binds DNA at stress response elements of responsive genes, inducing gene expression
YCR097W-A	0.160574	RPN4	YCR097W-A||S000007632|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; identified by homology to a hemiascomycetous yeast protein
YGR270C-A	0.160067	RPN4	YGR270C-A||S000028641|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified ORF YTA7/YGR270W
YDR426C	0.158193	RPN4	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
YGR253C	0.157954	RPN4	YGR253C|PUP2|S000003485|Alpha 5 subunit of the 20S proteasome involved in ubiquitin-dependent catabolism; human homolog is subunit zeta
YGR139W	0.156974	RPN4	YGR139W||S000003371|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR264C	0.156855	RPN4	YGR264C|MES1|S000003496|Methionyl-tRNA synthetase, forms a complex with glutamyl-tRNA synthetase (Gus1p) and Arc1p, which increases the catalytic efficiency of both tRNA synthetases; also has a role in nuclear export of tRNAs
YBL022C	0.15679	RPN4	YBL022C|PIM1|S000000118|ATP-dependent Lon protease, involved in degradation of misfolded proteins in mitochondria; required for biogenesis and maintenance of mitochondria
YBL092W	0.155881	RPN4	YBL092W|RPL32|S000000188|Protein component of the large (60S) ribosomal subunit, has similarity to rat L32 ribosomal protein; overexpression disrupts telomeric silencing
YOR352W	0.155683	RPN4	YOR352W||S000005879|Putative protein of unknown function; expression levels regulated by Arg5,6p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YBR056W-A	0.155474	RPN4	YBR056W-A||S000028736|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YBR056C-B
YER188W	0.154957	RPN4	YER188W||S000000990|Hypothetical protein
YOR326W	0.154323	RPN4	YOR326W|MYO2|S000005853|One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle
YOL011W	0.15389	RPN4	YOL011W|PLB3|S000005371|Phospholipase B (lysophospholipase) involved in phospholipid metabolism; hydrolyzes phosphatidylinositol and phosphatidylserine and displays transacylase activity in vitro
YMR300C	0.151863	RPN4	YMR300C|ADE4|S000004915|Phosphoribosylpyrophosphate amidotransferase (PRPPAT; amidophosphoribosyltransferase), catalyzes first step of the 'de novo' purine nucleotide biosynthetic pathway
YOR324C	0.149805	RPN4	YOR324C|FRT1|S000005851|Tail-anchored endoplasmic reticulum membrane protein that is a substrate of the phosphatase calcineurin, interacts with homolog Frt2p, promotes cell growth in conditions of high Na+, alkaline pH, and cell wall stress
YPL121C	0.148783	RPN4	YPL121C|MEI5|S000006042|Meiosis specific protein involved in DMC1-dependent meiotic recombination, forms heterodimer with Sae3p; proposed to be an assembly factor for Dmc1p
YGR228W	0.148239	RPN4	YGR228W||S000003460|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF SMI1/YGR229C
YLR108C	0.147922	RPN4	YLR108C||S000004098|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YLR108C is not an esssential gene
YOR233W	0.147422	RPN4	YOR233W|KIN4|S000005759|Serine/threonine protein kinase that inhibits the mitotic exit network (MEN) when the spindle position checkpoint is activated; localized asymmetrically to mother cell cortex, spindle pole body and bud neck
YDL148C	0.146404	RPN4	YDL148C|NOP14|S000002307|Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA
YER063W	0.144844	RPN4	YER063W|THO1|S000000865|Conserved nuclear RNA-binding protein; specifically binds to transcribed chromatin in a THO- and RNA-dependent manner, genetically interacts with shuttling hnRNP NAB2; overproduction suppresses transcriptional defect caused by hpr1 mutation
YDR432W	0.14404	RPN4	YDR432W|NPL3|S000002840|RNA-binding protein that carries poly(A)+ mRNA from the nucleus into the cytoplasm; dissociation from mRNAs is promoted by Mtr10p; phosphorylated by Sky1p in the cytoplasm
YLR186W	0.143933	RPN4	YLR186W|EMG1|S000004176|Member of the alpha/beta knot fold methyltransferase superfamily; required for maturation of 18S rRNA and for 40S ribosome production; interacts with RNA and with S-adenosylmethionine; associates with spindle/microtubules; forms homodimers
YKL188C	0.143534	RPN4	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
YCR051W	0.143318	RPN4	YCR051W||S000000647|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; contains ankyrin (Ank) repeats; YCR051W is not an essential gene
YKL119C	0.142061	RPN4	YKL119C|VPH2|S000001602|Integral membrane protein required for vacuolar H+-ATPase (V-ATPase) function, although not an actual component of the V-ATPase complex; functions in the assembly of the V-ATPase; localized to the endoplasmic reticulum (ER)
YJL198W	0.141504	RPN4	YJL198W|PHO90|S000003734|Low-affinity phosphate transporter; deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth
YOR259C	0.140439	RPN4	YOR259C|RPT4|S000005785|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for spindle pole body duplication; localized mainly to the nucleus throughout the cell cycle
YOR250C	0.140336	RPN4	YOR250C|CLP1|S000005776|Subunit of cleavage factor I (CFI), involved in both the endonucleolyitc cleavage and polyadenylation steps of mRNA 3'-end maturation
YGR189C	0.140016	RPN4	YGR189C|CRH1|S000003421|Putative chitin transglycosidase, cell wall protein that functions in the transfer of chitin to beta(1-6)glucan; localizes to sites of polarized growth; expression is induced under cell wall stress conditions
YOR025W	0.139989	RPN4	YOR025W|HST3|S000005551|Member of the Sir2 family of NAD(+)-dependent protein deacetylases; involved along with Hst4p in telomeric silencing, cell cycle progression, radiation resistance, genomic stability and short-chain fatty acid metabolism
YFL021W	0.138114	RPN4	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
YOR070C	0.137846	RPN4	YOR070C|GYP1|S000005596|Cis-golgi GTPase-activating protein (GAP) for the Rab family members Ypt1p (in vivo) and for Ypt1p, Sec4p, Ypt7p, and Ypt51p (in vitro); involved in vesicle docking and fusion
YKR005C	0.137276	RPN4	YKR005C||S000001713|Putative protein of unknown function
YMR121C	0.137106	RPN4	YMR121C|RPL15B|S000004728|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Ap and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA
YLR257W	0.13655	RPN4	YLR257W||S000004247|Putative protein of unknown function
YPL075W	0.135878	RPN4	YPL075W|GCR1|S000005996|Transcriptional activator of genes involved in glycolysis; DNA-binding protein that interacts and functions with the transcriptional activator Gcr2p
YKL145W	0.135575	RPN4	YKL145W|RPT1|S000001628|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p
YDR187C	0.135163	RPN4	YDR187C||S000002595|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified, essential ORF CCT6/YDR188W
YJR052W	0.134376	RPN4	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
YGR270W	0.134109	RPN4	YGR270W|YTA7|S000003502|Protein that localizes to chromatin and has a role in regulation of histone gene expression; has a bromodomain-like region that interacts with the N-terminal tail of histone H3, and an ATPase domain; potentially phosphorylated by Cdc28p
YBL042C	0.133655	RPN4	YBL042C|FUI1|S000000138|High affinity uridine permease, localized to the plasma membrane; not involved in uracil transport
YDR092W	0.133486	RPN4	YDR092W|UBC13|S000002499|Ubiquitin-conjugating enzyme involved in the error-free DNA postreplication repair pathway; interacts with Mms2p to assemble ubiquitin chains at the Ub Lys-63 residue; DNA damage triggers redistribution from the cytoplasm to the nucleus
YJL159W	0.132727	RPN4	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
YDR394W	0.132582	RPN4	YDR394W|RPT3|S000002802|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; substrate of N-acetyltransferase B
YOR178C	0.132439	RPN4	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
YDL012C	0.132362	RPN4	YDL012C||S000002170|Plasma membrane protein of unknown function; YDL012C is not an essential gene
YFR020W	0.13234	RPN4	YFR020W||S000001916|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL075C	0.132096	RPN4	YGL075C|MPS2|S000003043|Essential membrane protein localized at the nuclear envelope and spindle pole body (SPB), required for insertion of the newly duplicated SPB into the nuclear envelope; potentially phosphorylated by Cdc28p
YDR099W	0.132053	RPN4	YDR099W|BMH2|S000002506|14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling
YDL011C	0.131681	RPN4	YDL011C||S000002169|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the uncharacterized ORF YDL010W
YJL024C	0.130461	RPN4	YJL024C|APS3|S000003561|Small subunit of the clathrin-associated adaptor complex AP-3, which is involved in vacuolar protein sorting; related to the sigma subunit of the mammalian clathrin AP-3 complex; suppressor of loss of casein kinase 1 function
YGR294W	0.130153	RPN4	YGR294W|PAU12|S000003526|Hypothetical protein
YDR035W	0.129735	RPN4	YDR035W|ARO3|S000002442|3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase, catalyzes the first step in aromatic amino acid biosynthesis and is feedback-inhibited by phenylalanine or high concentration of tyrosine or tryptophan
YER019C-A	0.129591	RPN4	YER019C-A|SBH2|S000002127|Ssh1p-Sss1p-Sbh2p complex component, involved in protein translocation into the endoplasmic reticulum; homologous to Sbh1p
YDR418W	0.127221	RPN4	YDR418W|RPL12B|S000002826|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow growth and slow translation; has similarity to E. coli L11 and rat L12 ribosomal proteins
YPL080C	0.127093	RPN4	YPL080C||S000006001|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR151C	0.126912	RPN4	YOR151C|RPB2|S000005677|RNA polymerase II second largest subunit B150, part of central core; similar to bacterial beta subunit
YDR430C	0.125994	RPN4	YDR430C|CYM1|S000002838|Lysine-specific metalloprotease of the mitochondrial intermembrane space, member of the pitrilysin family; degrades proteins and presequence peptides cleaved from imported proteins; required for normal mitochondrial morphology
YDL010W	0.125992	RPN4	YDL010W|GRX6|S000002168|Cis-golgi localized monothiol glutaredoxin that binds an iron-sulfur cluster; more similar in activity to dithiol than other monothiol glutaredoxins; involved in the oxidative stress response; functional overlap with GRX6
YLR387C	0.125696	RPN4	YLR387C|REH1|S000004379|Protein of unknown function, similar to Rei1p but not involved in bud growth; contains dispersed C2H2 zinc finger domains
YIL144W	0.125329	RPN4	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
YJL177W	0.125327	RPN4	YJL177W|RPL17B|S000003713|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Ap and has similarity to E. coli L22 and rat L17 ribosomal proteins
YPR108W	0.124359	RPN4	YPR108W|RPN7|S000006312|Essential, non-ATPase regulatory subunit of the 26S proteasome, similar to another S. cerevisiae regulatory subunit, Rpn5p, as well as to mammalian proteasome subunits
YNL312W	0.124349	RPN4	YNL312W|RFA2|S000005256|Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination
YOL085C	0.124302	RPN4	YOL085C||S000005445|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; partially overlaps the dubious gene YOL085W-A
YOL100W	0.123677	RPN4	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
YLR134W	0.12322	RPN4	YLR134W|PDC5|S000004124|Minor isoform of pyruvate decarboxylase, key enzyme in alcoholic fermentation, decarboxylates pyruvate to acetaldehyde, regulation is glucose- and ethanol-dependent, repressed by thiamine, involved in amino acid catabolism
YDL097C	0.123173	RPN4	YDL097C|RPN6|S000002255|Essential, non-ATPase regulatory subunit of the 26S proteasome lid required for the assembly and activity of the 26S proteasome; the human homolog (S9 protein) partially rescues Rpn6p depletion
YIL079C	0.12276	RPN4	YIL079C|AIR1|S000001341|RING finger protein that interacts with the arginine methyltransferase Hmt1p to regulate methylation of Npl3p, which modulates Npl3p function in mRNA processing and export; has similarity to Air2p
YOR023C	0.122528	RPN4	YOR023C|AHC1|S000005549|Subunit of the Ada histone acetyltransferase complex, required for structural integrity of the complex
YOL105C	0.12223	RPN4	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
YDR049W	0.120752	RPN4	YDR049W||S000002456|Zinc finger protein; putative transcription factor that may interact with proteins involved in histone acetylation or deacetylation; may be involved in altering acetylation on histone lysines
YFL016C	0.119928	RPN4	YFL016C|MDJ1|S000001878|Co-chaperone that stimulates the ATPase activity of the HSP70 protein Ssc1p; involved in protein folding/refolding in the mitochodrial matrix; required for proteolysis of misfolded proteins; member of the HSP40 (DnaJ) family of chaperones
YER164W	0.119807	RPN4	YER164W|CHD1|S000000966|Nucleosome remodeling factor that functions in regulation of transcription elongation; contains a chromo domain, a helicase domain and a DNA-binding domain; component of both the SAGA and SLIK complexes
YGR249W	0.119374	RPN4	YGR249W|MGA1|S000003481|Protein similar to heat shock transcription factor; multicopy suppressor of pseudohyphal growth defects of ammonium permease mutants
YML113W	0.118612	RPN4	YML113W|DAT1|S000004581|DNA binding protein that recognizes oligo(dA).oligo(dT) tracts; Arg side chain in its N-terminal pentad Gly-Arg-Lys-Pro-Gly repeat is required for DNA-binding; not essential for viability
YMR016C	0.11798	RPN4	YMR016C|SOK2|S000004618|Nuclear protein that plays a regulatory role in the cyclic AMP (cAMP)-dependent protein kinase (PKA) signal transduction pathway; negatively regulates pseudohyphal differentiation; homologous to several transcription factors
YGL097W	0.117705	RPN4	YGL097W|SRM1|S000003065|Nucleotide exchange factor for Gsp1p, localizes to the nucleus, required for nucleocytoplasmic trafficking of macromolecules; suppressor of the pheromone response pathway; potentially phosphorylated by Cdc28p
YLR328W	0.117301	RPN4	YLR328W|NMA1|S000004320|Nicotinic acid mononucleotide adenylyltransferase, involved in pathways of NAD biosynthesis, including the de novo, NAD(+) salvage, and nicotinamide riboside salvage pathways
YJL111W	0.11474	RPN4	YJL111W|CCT7|S000003647|Subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p, required for the assembly of actin and tubulins in vivo
YLR247C	0.114583	RPN4	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
YCR099C	0.113977	RPN4	YCR099C||S000000696|Putative protein of unknown function
YBR042C	0.113894	RPN4	YBR042C|CST26|S000000246|Protein of unknown function, affects chromosome stability when overexpressed
YLR176C	0.11362	RPN4	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
YDR048C	0.11308	RPN4	YDR048C||S000002455|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR293C	0.112859	RPN4	YGR293C||S000003525|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YGR294W
YBR198C	0.111419	RPN4	YBR198C|TAF5|S000000402|Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification
YBR081C	0.111108	RPN4	YBR081C|SPT7|S000000285|Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex; also present as a C-terminally truncated form in the SLIK/SALSA transcriptional regulatory complex
YGL209W	0.110164	RPN4	YGL209W|MIG2|S000003177|Protein containing zinc fingers, involved in repression, along with Mig1p, of SUC2 (invertase) expression by high levels of glucose; binds to Mig1p-binding sites in SUC2 promoter
YKL154W	0.109965	RPN4	YKL154W|SRP102|S000001637|Signal recognition particle (SRP) receptor beta subunit; involved in SRP-dependent protein targeting; anchors Srp101p to the ER membrane
YDL100C	0.109418	RPN4	YDL100C|GET3|S000002258|Guanine nucleotide exchange factor for Gpa1p; amplifies G protein signaling; subunit of the GET complex, which is involved in Golgi to ER trafficking; has low-level ATPase activity and is involved in resistance to heat and metal stress
YFR016C	0.107622	RPN4	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
YIL143C	0.107316	RPN4	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
YGR144W	0.107243	RPN4	YGR144W|THI4|S000003376|Thiazole synthase, catalyzes formation of the thiazole moiety of thiamin pyrophosphate; required for thiamine biosynthesis and for mitochondrial genome stability
YGR095C	0.106995	RPN4	YGR095C|RRP46|S000003327|Protein involved in rRNA processing; component of the exosome 3->5 exonuclease complex
YOR005C	0.106854	RPN4	YOR005C|DNL4|S000005531|DNA ligase required for nonhomologous end-joining (NHEJ), forms stable heterodimer with required cofactor Lif1p, interacts with Nej1p; involved in meiosis, not essential for vegetative growth
YML034W	0.106724	RPN4	YML034W|SRC1|S000004497|Inner nuclear membrane (INM) protein with a putative role in sister chromatid segregation, potentially phosphorylated by Cdc28p; contains helix-extension-helix (HEH) motif, nuclear localization signal sequence
YOR028C	0.106455	RPN4	YOR028C|CIN5|S000005554|Basic leucine zipper transcriptional factor of the yAP-1 family that mediates pleiotropic drug resistance and salt tolerance; localizes constitutively to the nucleus
YER146W	0.104528	RPN4	YER146W|LSM5|S000000948|Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA
YPL079W	0.10444	RPN4	YPL079W|RPL21B|S000006000|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl21Ap and has similarity to rat L21 ribosomal protein
YLR263W	0.104138	RPN4	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
YOR153W	0.103741	RPN4	YOR153W|PDR5|S000005679|Plasma membrane ATP-binding cassette (ABC) transporter, short-lived multidrug transporter actively regulated by Pdr1p; also involved in steroid transport, cation resistance, and cellular detoxification during exponential growth
YOR368W	0.103216	RPN4	YOR368W|RAD17|S000005895|Checkpoint protein, involved in the activation of the DNA damage and meiotic pachytene checkpoints; with Mec3p and Ddc1p, forms a clamp that is loaded onto partial duplex DNA; homolog of human and S. pombe Rad1 and U. maydis Rec1 proteins
YGL150C	0.102241	RPN4	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
YOL014W	0.102058	RPN4	YOL014W||S000005374|Putative protein of unknown function
YML034C-A	0.101898	RPN4	YML034C-A||S000004499|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR135W	0.101466	RPN4	YGR135W|PRE9|S000003367|Alpha 3 subunit of the 20S proteasome, the only nonessential 20S subunit; may be replaced by the alpha 4 subunit (Pre6p) under stress conditions to create a more active proteasomal isoform
YLR314C	0.10103	RPN4	YLR314C|CDC3|S000004306|Component of the septin ring of the mother-bud neck that is required for cytokinesis; septins recruit proteins to the neck and can act as a barrier to diffusion at the membrane, and they comprise the 10nm filaments seen with EM
YGR039W	0.100871	RPN4	YGR039W||S000003271|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the Autonomously Replicating Sequence ARS722
YER094C	0.100281	RPN4	YER094C|PUP3|S000000896|Beta 3 subunit of the 20S proteasome involved in ubiquitin-dependent catabolism; human homolog is subunit C10
YOL094C	0.100247	RPN4	YOL094C|RFC4|S000005454|Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon
YEL039C	0.099957	RPN4	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
YGL253W	0.0997594	RPN4	YGL253W|HXK2|S000003222|Hexokinase isoenzyme 2 that catalyzes phosphorylation of glucose in the cytosol; predominant hexokinase during growth on glucose; functions in the nucleus to repress expression of HXK1 and GLK1 and to induce expression of its own gene
YKL063C	0.0995328	RPN4	YKL063C||S000001546|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the Golgi
YGR090W	0.0993729	RPN4	YGR090W|UTP22|S000003322|Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data
YHR134W	0.0980736	RPN4	YHR134W|WSS1|S000001176|Sumoylated protein of unknown function, identified based on genetic interactions with SMT3; UV-sensitive mutant phenotype and genetic interactions suggest a role in the DNA damage response, processing stalled or collapsed replication forks
YFL056C	0.0971728	RPN4	YFL056C|AAD6|S000001838|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase, involved in the oxidative stress response
YBR162W-A	0.0968156	RPN4	YBR162W-A|YSY6|S000002158|Protein whose expression suppresses a secretory pathway mutation in E. coli; has similarity to the mammalian RAMP4 protein involved in secretion
YGL118C	0.0966932	RPN4	YGL118C||S000003086|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR180C	0.0952205	RPN4	YMR180C|CTL1|S000004792|RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm
YOR097C	0.0952033	RPN4	YOR097C||S000005623|Putative protein of unknown function; identified as interacting with Hsp82p in a high-throughput two-hybrid screen; YOR097C is not an essential gene
YOL045W	0.0949365	RPN4	YOL045W|PSK2|S000005405|One of two (see also PSK1) PAS domain containing S/T protein kinases; regulates sugar flux and translation in response to an unknown metabolite by phosphorylating Ugp1p and Gsy2p (sugar flux) and Caf20p, Tif11p and Sro9p (translation)
YJL160C	0.0944622	RPN4	YJL160C||S000003696|Putative protein of unknown function; member of the PIR (proteins with internal repeats) family of cell wall proteins; non-essential gene that is required for sporulation; mRNA is weakly cell cycle regulated, peaking in mitosis
YCR092C	0.0943101	RPN4	YCR092C|MSH3|S000000688|Mismatch repair protein, forms dimers with Msh2p that mediate repair of insertion or deletion mutations and removal of nonhomologous DNA ends, contains a PCNA (Pol30p) binding motif required for genome stability
YDL007C-A	0.094008	RPN4	YDL007C-A||S000113557|Putative protein of unknown function
YPR121W	0.0932378	RPN4	YPR121W|THI22|S000006325|Protein with similarity to hydroxymethylpyrimidine phosphate kinases; member of a gene family with THI20 and THI21; not required for thiamine biosynthesis
YDL134C	0.0931875	RPN4	YDL134C|PPH21|S000002292|Catalytic subunit of protein phosphatase 2A, functionally redundant with Pph22p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis
YPL111W	0.0921446	RPN4	YPL111W|CAR1|S000006032|Arginase, responsible for arginine degradation, expression responds to both induction by arginine and nitrogen catabolite repression; disruption enhances freeze tolerance
YOR388C	0.0915871	RPN4	YOR388C|FDH1|S000005915|NAD(+)-dependent formate dehydrogenase, may protect cells from exogenous formate
YJR128W	0.0898657	RPN4	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
YEL068C	0.089682	RPN4	YEL068C||S000000794|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR373C	0.0888711	RPN4	YLR373C|VID22|S000004365|Glycosylated integral membrane protein localized to the plasma membrane; plays a role in fructose-1,6-bisphosphatase (FBPase) degradation; involved in FBPase transport from the cytosol to Vid (vacuole import and degradation) vesicles
YLR437C-A	0.0873476	RPN4	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
YPL049C	0.0872772	RPN4	YPL049C|DIG1|S000005970|Regulatory protein of unknown function, constitutively-expressed, involved in the regulation of mating-specific genes and the invasive growth pathway, required for MAP-kinase imposed repression, inhibits pheromone-responsive transcription
YDR194C	0.0870955	RPN4	YDR194C|MSS116|S000002602|DEAD-box protein required for efficient splicing of mitochondrial Group I and II introns; non-polar RNA helicase that also facilities strand annealing
YBR199W	0.0862415	RPN4	YBR199W|KTR4|S000000403|Putative mannosyltransferase involved in protein glycosylation; member of the KRE2/MNT1 mannosyltransferase family
YML031W	0.0851769	RPN4	YML031W|NDC1|S000004493|Nuclear envelope protein with multiple putative transmembrane domains, required for nuclear pore complex assembly and spindle pole body duplication; required for meiosis II
YOR290C	0.0839568	RPN4	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
YHL002C-A	0.0838594	RPN4	YHL002C-A||S000028770|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR154C	0.0831869	RPN4	YLR154C|RNH203|S000004144|Ribonuclease H2 subunit, required for RNase H2 activity
YBR203W	0.0831498	RPN4	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
YNL324W	0.082698	RPN4	YNL324W||S000005268|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKL155C	0.08263	RPN4	YKL155C|RSM22|S000001638|Mitochondrial ribosomal protein of the small subunit
YOR117W	0.0823748	RPN4	YOR117W|RPT5|S000005643|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; recruited to the GAL1-10 promoter region upon induction of transcription
YBL077W	0.0809423	RPN4	YBL077W||S000000173|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene ILS1/YBL076C
YIL005W	0.0804535	RPN4	YIL005W|EPS1|S000001267|ER protein with chaperone and co-chaperone activity, involved in retention of resident ER proteins; has a role in recognizing proteins targeted for ER-associated degradation (ERAD), member of the protein disulfide isomerase family
YKR079C	0.0797529	RPN4	YKR079C|TRZ1|S000001787|tRNase Z, involved in RNA processing, has two putative nucleotide triphosphate-binding motifs (P-loop) and a conserved histidine motif, homolog of the human candidate prostate cancer susceptibility gene ELAC2
YIL075C	0.0795494	RPN4	YIL075C|RPN2|S000001337|Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p
YNR069C	0.0793429	RPN4	YNR069C|BSC5|S000005352|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YJL092W	0.0792714	RPN4	YJL092W|SRS2|S000003628|DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination
YER016W	0.0788079	RPN4	YER016W|BIM1|S000000818|Microtubule-binding protein that together with Kar9p makes up the cortical microtubule capture site and delays the exit from mitosis when the spindle is oriented abnormally
YPL255W	0.0783305	RPN4	YPL255W|BBP1|S000006176|Protein required for the spindle pole body (SPB) duplication, localized at the central plaque periphery; forms a complex with a nuclear envelope protein Mps2p and SPB components Spc29p and Kar1p; required for mitotic functions of Cdc5p
YMR033W	0.0777956	RPN4	YMR033W|ARP9|S000004636|Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation
YGL203C	0.0750065	RPN4	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
YMR207C	0.0748728	RPN4	YMR207C|HFA1|S000004820|Mitochondrial acetyl-coenzyme A carboxylase, catalyzes the production of malonyl-CoA in mitochondrial fatty acid biosynthesis
YDL074C	0.0748524	RPN4	YDL074C|BRE1|S000002232|E3 ubiquitin ligase for Rad6p, required for the ubiquitination of histone H2B, recruitment of Rad6p to promoter chromatin and subsequent methylation of histone H3 (on K4 and K79), contains RING finger domain
YJL162C	0.0747899	RPN4	YJL162C|JJJ2|S000003698|Protein of unknown function, contains a J-domain, which is a region with homology to the E. coli DnaJ protein
YJL101C	0.0747788	RPN4	YJL101C|GSH1|S000003637|Gamma glutamylcysteine synthetase catalyzes the first step in glutathione (GSH) biosynthesis; expression induced by oxidants, cadmium, and mercury
YOL023W	0.074496	RPN4	YOL023W|IFM1|S000005383|Mitochondrial translation initiation factor 2
YDL132W	0.0744428	RPN4	YDL132W|CDC53|S000002290|Cullin, structural protein of SCF complexes (which also contain Skp1p, Cdc34p, Hrt1p and an F-box protein) involved in ubiquitination; SCF promotes the G1-S transition by targeting G1 cyclins and the Cln-CDK inhibitor Sic1p for degradation
YPR052C	0.0741665	RPN4	YPR052C|NHP6A|S000006256|High-mobility group non-histone chromatin protein, functionally redundant with Nhp6Bp; homologous to mammalian high mobility group proteins 1 and 2; acts to recruit transcription factor Rcs1p to certain promoters
YNL199C	0.073131	RPN4	YNL199C|GCR2|S000005143|Transcriptional activator of genes involved in glycolysis; interacts and functions with the DNA-binding protein Gcr1p
YNR006W	0.0730256	RPN4	YNR006W|VPS27|S000005289|Endosomal protein that forms a complex with Hse1p; required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated proteins destined for degradation; has Ubiquitin Interaction Motifs which bind ubiquitin (Ubi4p)
YJR055W	0.0724333	RPN4	YJR055W|HIT1|S000003816|Protein of unknown function, required for growth at high temperature
YDR429C	0.0722259	RPN4	YDR429C|TIF35|S000002837|Subunit of the core complex of translation initiation factor 3(eIF3), which is essential for translation
YPL279C	0.0720103	RPN4	YPL279C||S000006200|Putative protein of unknown function
YGR040W	0.0716562	RPN4	YGR040W|KSS1|S000003272|Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains
YNR005C	0.0714865	RPN4	YNR005C||S000005288|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YIR021W	0.0699997	RPN4	YIR021W|MRS1|S000001460|Protein required for the splicing of two mitochondrial group I introns (BI3 in COB and AI5beta in COX1); forms a splicing complex, containing four subunits of Mrs1p and two subunits of the BI3-encoded maturase, that binds to the BI3 RNA
YOR185C	0.0695987	RPN4	YOR185C|GSP2|S000005711|GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; interacts with Kap121p, Kap123p and Pdr6p (karyophilin betas); Gsp1p homolog that is not required for viability
YDR089W	0.0690983	RPN4	YDR089W||S000002496|Protein of unknown function; deletion confers resistance to Nickel
YNR032C-A	0.068496	RPN4	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
YJL153C	0.0679467	RPN4	YJL153C|INO1|S000003689|Inositol 1-phosphate synthase, involved in synthesis of inositol phosphates and inositol-containing phospholipids; transcription is coregulated with other phospholipid biosynthetic genes by Ino2p and Ino4p, which bind the UASINO DNA element
YOR342C	0.0675584	RPN4	YOR342C||S000005869|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus
YGR123C	0.0669606	RPN4	YGR123C|PPT1|S000003355|Protein serine/threonine phosphatase with similarity to human phosphatase PP5; present in both the nucleus and cytoplasm; expressed during logarithmic growth; computational analyses suggest roles in phosphate metabolism and rRNA processing
YGL179C	0.0663606	RPN4	YGL179C|TOS3|S000003147|Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome
YNL138W-A	0.0662608	RPN4	YNL138W-A|YSF3|S000028509|Component of the U2 snRNP, associated with the SF3b complex; conserved in Ashbya gossypii
YLL028W	0.0660539	RPN4	YLL028W|TPO1|S000003951|Polyamine transporter that recognizes spermine, putrescine, and spermidine; catalyzes uptake of polyamines at alkaline pH and excretion at acidic pH; phosphorylation enhances activity and sorting to the plasma membrane
YML063W	0.0658745	RPN4	YML063W|RPS1B|S000004528|Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein
YFR052W	0.0654658	RPN4	YFR052W|RPN12|S000001948|Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p
YHR157W	0.0648025	RPN4	YHR157W|REC104|S000001200|Protein involved in early stages of meiotic recombination; required for meiotic crossing over; forms a complex with Rec102p and Spo11p necessary during the initiation of recombination
YGL177W	0.0642563	RPN4	YGL177W||S000003145|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR440W	0.064162	RPN4	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
YOR262W	0.0641207	RPN4	YOR262W||S000005788|Protein of unknown function required for establishment of sister chromatid cohesion; contains an ATP/GTP binding site motif; similar to YLR243W and is highly conserved across species and homologous to human gene GPN2/ATPBD1B
YPR148C	0.0637647	RPN4	YPR148C||S000006352|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YPR120C	0.0637102	RPN4	YPR120C|CLB5|S000006324|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 phase
YHR085W	0.0636847	RPN4	YHR085W|IPI1|S000001127|Essential component of the Rix1 complex (with Rix1p and Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles
YCL043C	0.0636102	RPN4	YCL043C|PDI1|S000000548|Protein disulfide isomerase, multifunctional protein resident in the endoplasmic reticulum lumen, essential for the formation of disulfide bonds in secretory and cell-surface proteins, unscrambles non-native disulfide bonds
YOR291W	0.0633548	RPN4	YOR291W||S000005817|Putative protein of unknown function; shares sequence similarity with the type V P-type ATPase Spf1p; YOR291W is not an essential protein
YJL011C	0.0632743	RPN4	YJL011C|RPC17|S000003548|RNA polymerase III subunit C17; physically interacts with C31, C11, and TFIIIB70; may be involved in the recruitment of pol III by the preinitiation complex
YHR091C	0.0630988	RPN4	YHR091C|MSR1|S000001133|Mitochondrial arginyl-tRNA synthetase
YBL054W	0.0630901	RPN4	YBL054W||S000000150|Protein of unknown function involved in rRNA and ribosome biosynthesis
YKL211C	0.0628305	RPN4	YKL211C|TRP3|S000001694|Bifunctional enzyme exhibiting both indole-3-glycerol-phosphate synthase and anthranilate synthase activities, forms multifunctional hetero-oligomeric anthranilate synthase:indole-3-glycerol phosphate synthase enzyme complex with Trp2p
YJR090C	0.0626875	RPN4	YJR090C|GRR1|S000003850|F-box protein component of the SCF ubiquitin-ligase complex; involved in carbon catabolite repression, glucose-dependent divalent cation transport, high-affinity glucose transport, morphogenesis, and sulfite detoxification
YOL098C	0.0625416	RPN4	YOL098C||S000005458|Putative metalloprotease
YDR188W	0.0618577	RPN4	YDR188W|CCT6|S000002596|Subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p, essential protein that is required for the assembly of actin and tubulins in vivo; contains an ATP-binding motif
YKL165C-A	0.0617518	RPN4	YKL165C-A||S000007617|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL044C	0.0615663	RPN4	YIL044C|AGE2|S000001306|ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector, involved in Trans-Golgi-Network (TGN) transport; contains C2C2H2 cysteine/histidine motif
YNL183C	0.0611142	RPN4	YNL183C|NPR1|S000005127|Protein kinase that stabilizes several plasma membrane amino acid transporters by antagonizing their ubiquitin-mediated degradation
YER143W	0.0608546	RPN4	YER143W|DDI1|S000000945|DNA damage-inducible v-SNARE binding protein, contains a ubiquitin-associated (UBA) domain, may act as a negative regulator of constitutive exocytosis, may play a role in S-phase checkpoint control
YOR313C	0.0608136	RPN4	YOR313C|SPS4|S000005840|Protein whose expression is induced during sporulation; not required for sporulation; heterologous expression in E. coli induces the SOS response that senses DNA damage
YMR068W	0.060228	RPN4	YMR068W|AVO2|S000004672|Component of a complex containing the Tor2p kinase and other proteins, which may have a role in regulation of cell growth
YDR152W	0.0586736	RPN4	YDR152W|GIR2|S000002559|Highly-acidic cytoplasmic RWD domain-containing protein of unknown function, sensitive to proteolysis, N-terminal region has high content of acidic amino acid residues, putative IUP (intrinsically unstructured protein)
YBR155W	0.0586006	RPN4	YBR155W|CNS1|S000000359|TPR-containing co-chaperone; binds both Hsp82p (Hsp90) and Ssa1p (Hsp70) and stimulates the ATPase activity of SSA1, ts mutants reduce Hsp82p function while over expression suppresses the phenotypes of an HSP82 ts allele and a cpr7 deletion
YKL189W	0.0578178	RPN4	YKL189W|HYM1|S000001672|Component of the RAM signaling network that is involved in regulation of Ace2p activity and cellular morphogenesis, interacts with Kic1p and Sog2p, localizes to sites of polarized growth during budding and during the mating response
YBR157C	0.0577742	RPN4	YBR157C|ICS2|S000000361|Protein of unknown function; null mutation does not confer any obvious defects in growth, spore germination, viability, or carbohydrate utilization
YBL027W	0.0577727	RPN4	YBL027W|RPL19B|S000000123|Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl19Ap and has similarity to rat L19 ribosomal protein; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal
YLR117C	0.0574498	RPN4	YLR117C|CLF1|S000004107|Essential splicesome assembly factor; contains multiple tetratricopeptide repeat (TPR) protein-binding motifs and interacts specifically with many spliceosome components, may serve as a scaffold during splicesome assembly
YDR359C	0.0572083	RPN4	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
YDL009C	0.057157	RPN4	YDL009C||S000002167|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YDL010W; YDL009C is not an essential gene
YOR030W	0.0568336	RPN4	YOR030W|DFG16|S000005556|Probable multiple transmembrane protein, involved in diploid invasive and pseudohyphal growth upon nitrogen starvation; required for accumulation of processed Rim101p
YER014C-A	0.0566971	RPN4	YER014C-A|BUD25|S000007590|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YNL208W	0.0563377	RPN4	YNL208W||S000005152|Protein of unknown function; may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in purified mitochondria in high-throughput studies; potential orthologs found in other fungi
YKR010C	0.0561347	RPN4	YKR010C|TOF2|S000001718|Nonessential mitochondrial protein of unknown function with sequence similarity to Net1p; identified as a topoisomerase I (Top1p) binding protein; displays synthetic genetic interactions with TOP1 and HPR1
YFR021W	0.0560251	RPN4	YFR021W|ATG18|S000001917|Phosphoinositide binding protein required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; binds both phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol 3-phosphate; WD-40 repeat protein
YDR072C	0.0557521	RPN4	YDR072C|IPT1|S000002479|Inositolphosphotransferase 1, involved in synthesis of mannose-(inositol-P)2-ceramide (M(IP)2C), which is the most abundant sphingolipid in cells, mutation confers resistance to the antifungals syringomycin E and DmAMP1 in some growth media
YCR098C	0.0555548	RPN4	YCR098C|GIT1|S000000695|Plasma membrane permease, mediates uptake of glycerophosphoinositol and glycerophosphocholine as sources of the nutrients inositol and phosphate; expression and transport rate are regulated by phosphate and inositol availability
YLL019C	0.0550999	RPN4	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
YHR129C	0.0548354	RPN4	YHR129C|ARP1|S000001171|Actin-related protein of the dynactin complex; required for spindle orientation and nuclear migration; putative ortholog of mammalian centractin
YLR401C	0.0543956	RPN4	YLR401C|DUS3|S000004393|Dihydrouridine synthase, member of a widespread family of conserved proteins including Smm1p, Dus1p, and Dus4p; contains a consensus oleate response element (ORE) in its promoter region
YGL074C	0.0543306	RPN4	YGL074C||S000003042|Dubious open reading frame unlikely to encode a functional protein; overlaps 5' end of essential HSF1 gene encoding heat shock transcription factor
YMR298W	0.0543218	RPN4	YMR298W|LIP1|S000004913|Ceramide synthase subunit; single-span ER membrane protein associated with Lag1p and Lac1p and required for ceramide synthase activity, null mutant grows extremely slowly and is defective in ceramide synthesis
YBR023C	0.0537944	RPN4	YBR023C|CHS3|S000000227|Chitin synthase III, catalyzes the transfer of N-acetylglucosamine (GlcNAc) to chitin; required for synthesis of the majority of cell wall chitin, the chitin ring during bud emergence, and spore wall chitosan
YIL132C	0.0537263	RPN4	YIL132C|CSM2|S000001394|Protein required for accurate chromosome segregation during meiosis
YLR109W	0.0532736	RPN4	YLR109W|AHP1|S000004099|Thiol-specific peroxiredoxin, reduces hydroperoxides to protect against oxidative damage; function in vivo requires covalent conjugation to Urm1p
YHR178W	0.0531569	RPN4	YHR178W|STB5|S000001221|Activator of multidrug resistance genes, forms a heterodimer with Pdr1p; contains a Zn(II)2Cys6 zinc finger domain that interacts with a PDRE (pleotropic drug resistance element) in vitro; binds Sin3p in a two-hybrid assay
YPL009C	0.0531293	RPN4	YPL009C||S000005930|Protein of unknown function; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL009C is not an essential gene
YDL224C	0.0530164	RPN4	YDL224C|WHI4|S000002383|Putative RNA binding protein and partially redundant Whi3p homolog that regulates the cell size requirement for passage through Start and commitment to cell division
YHR205W	0.0530114	RPN4	YHR205W|SCH9|S000001248|Protein kinase involved in transcriptional activation of osmostress-responsive genes; regulates G1 progression, cAPK activity, nitrogen activation of the FGM pathway; involved in life span regulation; homologous to mammalian Akt/PKB
YJL205C	0.0528628	RPN4	YJL205C|NCE101|S000003742|Protein of unknown function, involved in secretion of proteins that lack classical secretory signal sequences
YNL198C	0.0526925	RPN4	YNL198C||S000005142|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR063W	0.0520892	RPN4	YOR063W|RPL3|S000005589|Protein component of the large (60S) ribosomal subunit, has similarity to E. coli L3 and rat L3 ribosomal proteins; involved in the replication and maintenance of killer double stranded RNA virus
YDR044W	0.0515525	RPN4	YDR044W|HEM13|S000002451|Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)
YPL112C	0.0509959	RPN4	YPL112C|PEX25|S000006033|Peripheral peroxisomal membrane peroxin required for the regulation of peroxisome size and maintenance, recruits GTPase Rho1p to peroxisomes, induced by oleate, interacts with homologous protein Pex27p
YMR123W	0.050965	RPN4	YMR123W|PKR1|S000004730|V-ATPase assembly factor, functions with other V-ATPase assembly factors in the ER to efficiently assemble the V-ATPase membrane sector (V0); overproduction confers resistance to Pichia farinosa killer toxin
YNL118C	0.0507496	RPN4	YNL118C|DCP2|S000005062|Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family
YLR262C-A	0.0502953	RPN4	YLR262C-A|TMA7|S000007246|Protein of unknown that associates with ribosomes; null mutant exhibits translation defects, altered polyribosome profiles, and resistance to the translation inhibitor anisomcyin
YDL140C	0.0502887	RPN4	YDL140C|RPO21|S000002299|RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime
YIR014W	0.0498154	RPN4	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
YPR019W	0.0492167	RPN4	YPR019W|MCM4|S000006223|Essential helicase component of heterohexameric MCM2-7 complexes which bind pre-replication complexes on DNA and melt the DNA prior to replication; accumulates in the nucleus in G1; homolog of S. pombe Cdc21p
YGL190C	0.048857	RPN4	YGL190C|CDC55|S000003158|Non-essential regulatory subunit B of protein phosphatase 2A, which has multiple roles in mitosis and protein biosynthesis; involved in regulation of mitotic exit; found in the nucleus of most cells, also at the bud neck and at the bud tip
YLR420W	0.0482577	RPN4	YLR420W|URA4|S000004412|Dihydroorotase, catalyzes the third enzymatic step in the de novo biosynthesis of pyrimidines, converting carbamoyl-L-aspartate into dihydroorotate
YDR101C	0.047835	RPN4	YDR101C|ARX1|S000002508|Shuttling pre-60S factor; involved in the biogenesis of ribosomal large subunit biogenesis; interacts directly with Alb1; responsible for Tif6 recycling defects in absence of Rei1; associated with the ribosomal export complex
YGL239C	0.0477686	RPN4	YGL239C||S000003208|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene CSE1
YKR026C	0.047668	RPN4	YKR026C|GCN3|S000001734|Alpha subunit of the translation initiation factor eIF2B, the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a positive regulator of GCN4 expression
YBL078C	0.0470627	RPN4	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
YMR283C	0.0470517	RPN4	YMR283C|RIT1|S000004896|2'-O-ribosyl phosphate transferase, modifies the initiator methionine tRNA at position 64 to distinguish it from elongator methionine tRNA
YBR257W	0.0466539	RPN4	YBR257W|POP4|S000000461|Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursors to generate mature 5' ends; binds to the RPR1 RNA subunit in Rnase P
YGR020C	0.0465015	RPN4	YGR020C|VMA7|S000003252|Subunit F of the eight-subunit V1 peripheral membrane domain of vacuolar H+-ATPase (V-ATPase), an electrogenic proton pump found throughout the endomembrane system; required for the V1 domain to assemble onto the vacuolar membrane
YLR177W	0.0464324	RPN4	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
YBL061C	0.0463222	RPN4	YBL061C|SKT5|S000000157|Activator of Chs3p (chitin synthase III), recruits Chs3p to the bud neck via interaction with Bni4p; has similarity to Shc1p, which activates Chs3p during sporulation
YDL049C	0.0462332	RPN4	YDL049C|KNH1|S000002207|Protein with similarity to Kre9p, which is involved in cell wall beta 1,6-glucan synthesis; overproduction suppresses growth defects of a kre9 null mutant
YKL182W	0.0454323	RPN4	YKL182W|FAS1|S000001665|Beta subunit of fatty acid synthetase, which catalyzes the synthesis of long-chain saturated fatty acids; contains acetyltransacylase, dehydratase, enoyl reductase, malonyl transacylase, and palmitoyl transacylase activities
YLR167W	0.0450771	RPN4	YLR167W|RPS31|S000004157|Fusion protein that is cleaved to yield a ribosomal protein of the small (40S) subunit and ubiquitin; ubiquitin may facilitate assembly of the ribosomal protein into ribosomes; interacts genetically with translation factor eIF2B
YLR355C	0.0450743	RPN4	YLR355C|ILV5|S000004347|Acetohydroxyacid reductoisomerase, mitochondrial protein involved in branched-chain amino acid biosynthesis, also required for maintenance of wild-type mitochondrial DNA and found in mitochondrial nucleoids
YIR038C	0.0449116	RPN4	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
YDL008W	0.044814	RPN4	YDL008W|APC11|S000002166|Catalytic core subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition
YPR195C	0.0446131	RPN4	YPR195C||S000006399|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR047C	0.0445933	RPN4	YHR047C|AAP1|S000001089|Arginine/alanine aminopeptidase, overproduction stimulates glycogen accumulation
YML071C	0.0433383	RPN4	YML071C|COG8|S000004536|Component of the conserved oligomeric Golgi complex (Cog1p through Cog8p), a cytosolic tethering complex that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments
YOL054W	0.0432981	RPN4	YOL054W|PSH1|S000005415|Nuclear protein, putative RNA polymerase II elongation factor; isolated as Pob3p/Spt16p-binding protein
YJL222W	0.0432918	RPN4	YJL222W|VTH2|S000003758|Putative membrane glycoprotein with strong similarity to Vth1p and Pep1p/Vps10p, may be involved in vacuolar protein sorting
YMR195W	0.0431388	RPN4	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
YER020W	0.0422578	RPN4	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
YFL010W-A	0.0422211	RPN4	YFL010W-A|AUA1|S000001955|Protein required for the negative regulation by ammonia of Gap1p, which is a general amino acid permease
YML074C	0.0419446	RPN4	YML074C|FPR3|S000004539|Nucleolar peptidyl-prolyl cis-trans isomerase (PPIase); FK506 binding protein; phosphorylated by casein kinase II (Cka1p-Cka2p-Ckb1p-Ckb2p) and dephosphorylated by Ptp1p
YOL022C	0.0410709	RPN4	YOL022C|TSR4|S000005382|Cytoplasmic protein of unknown function; essential gene in S288C, and non-essential with reduced growth rate in CEN.PK2; Null mutant accumulates 20S pre-rRNA
YBR062C	0.0410095	RPN4	YBR062C||S000000266|Hypothetical protein
YDR151C	0.0409167	RPN4	YDR151C|CTH1|S000002558|Member of the CCCH zinc finger family; has similarity to mammalian Tis11 protein, which activates transcription and also has a role in mRNA degradation; may function with Tis11p in iron homeostasis
YPR193C	0.0404102	RPN4	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
YGL178W	0.0401728	RPN4	YGL178W|MPT5|S000003146|Member of the Puf family of RNA-binding proteins; binds to mRNAs encoding chromatin modifiers and spindle pole body components; involved in longevity, maintenance of cell wall integrity, and sensitivity to and recovery from pheromone arrest
YDR310C	0.0400029	RPN4	YDR310C|SUM1|S000002718|Transcriptional repressor required for mitotic repression of middle sporulation-specific genes; involved in telomere maintenance, regulated by the pachytene checkpoint
YLR113W	0.0397472	RPN4	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
YGR225W	0.0391087	RPN4	YGR225W|AMA1|S000003457|Activator of meiotic anaphase promoting complex (APC/C); Cdc20p family member; required for initiation of spore wall assembly; required for Clb1p degradation during meiosis
YHR212W-A	0.0390384	RPN4	YHR212W-A||S000028650|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YGL014W	0.0390205	RPN4	YGL014W|PUF4|S000002982|Member of the PUF protein family, which is defined by the presence of Pumilio homology domains that confer RNA binding activity; preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors
YJR061W	0.0390096	RPN4	YJR061W||S000003822|Putative protein of unknown function; non-essential gene with similarity to Mnn4, a putative membrane protein involved in glycosylation; transcription repressed by Rm101p
YKL104C	0.0389376	RPN4	YKL104C|GFA1|S000001587|Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis
YKL202W	0.0378475	RPN4	YKL202W||S000001685|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR046W	0.0374257	RPN4	YGR046W|TAM41|S000003278|Mitochondrial protein involved in protein import into the mitochondrial matrix; maintains the functional integrity of the TIM23 protein translocator complex; viability of null mutant is strain-dependent; mRNA is targeted to the bud
YPR192W	0.0373971	RPN4	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
YJL006C	0.0373965	RPN4	YJL006C|CTK2|S000003543|Beta subunit of C-terminal domain kinase I (CTDK-I), which phosphorylates the C-terminal repeated domain of the RNA polymerase II large subunit (Rpo21p) to affect both transcription and pre-mRNA 3' end processing; has similarity to cyclins
YNL271C	0.0372896	RPN4	YNL271C|BNI1|S000005215|Formin, nucleates the formation of linear actin filaments, involved in cell processes such as budding and mitotic spindle orientation which require the formation of polarized actin cables, functionally redundant with BNR1
YPR021C	0.0372337	RPN4	YPR021C|AGC1|S000006225|Mitochondrial amino acid transporter, acts both as a glutamate uniporter and as an aspartate-glutamate exchanger; involved in nitrogen metabolism and nitrogen compound biosynthesis
YOR008C-A	0.0368973	RPN4	YOR008C-A||S000006431|Putative protein of unknown function, includes a potential transmembrane domain; deletion results in slightly lengthened telomeres
YDR212W	0.0367071	RPN4	YDR212W|TCP1|S000002620|Alpha subunit of chaperonin-containing T-complex, which mediates protein folding in the cytosol; involved in maintenance of actin cytoskeleton; homolog to Drosophila melanogaster and mouse tailless complex polypeptide
YHR181W	0.0366248	RPN4	YHR181W|SVP26|S000001224|Integral membrane protein of the early Golgi apparatus and endoplasmic reticulum, involved in COP II vesicle transport; may also function to promote retention of proteins in the early Golgi compartment
YPL008W	0.0363942	RPN4	YPL008W|CHL1|S000005929|Conserved nuclear protein required to establish sister-chromatid pairing during S-phase, probable DNA helicase with similarity to human BACH1, which associates with tumor suppressor BRCA1; associates with acetyltransferase Ctf7p
YML114C	0.0363158	RPN4	YML114C|TAF8|S000004582|TFIID subunit (65 kDa), involved in RNA polymerase II transcription initiation
YPR138C	0.0361342	RPN4	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
YBR201W	0.0351738	RPN4	YBR201W|DER1|S000000405|Endoplasmic reticulum membrane protein, required for ER-associated protein degradation of misfolded or unassembled proteins; N- and C- termini protrude into the cytoplasm, has similarity to Dfm1p
YKL005C	0.034961	RPN4	YKL005C|BYE1|S000001488|Negative regulator of transcription elongation, contains a TFIIS-like domain and a PHD finger, multicopy suppressor of temperature-sensitive ess1 mutations, probably binds RNA polymerase II large subunit
YDR473C	0.0346717	RPN4	YDR473C|PRP3|S000002881|Splicing factor, component of the U4/U6-U5 snRNP complex
YAR019W-A	0.0341906	RPN4	YAR019W-A||S000028735|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL134W	0.0338129	RPN4	YIL134W|FLX1|S000001396|Protein required for transport of flavin adenine dinucleotide (FAD), a synthesis product of riboflavin, across the mitochondrial membrane
YNL331C	0.033724	RPN4	YNL331C|AAD14|S000005275|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YLR094C	0.0337174	RPN4	YLR094C|GIS3|S000004084|Protein of unknown function
YGR251W	0.0333703	RPN4	YGR251W||S000003483|Putative protein of unknown function; deletion mutant has defects in pre-rRNA processing; green fluorescent protein (GFP)-fusion protein localizes to both the nucleus and the nucleolus; YGR251W is an essential gene
YER165W	0.0328814	RPN4	YER165W|PAB1|S000000967|Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G
YDL191W	0.0328544	RPN4	YDL191W|RPL35A|S000002350|Protein component of the large (60S) ribosomal subunit, identical to Rpl35Bp and has similarity to rat L35 ribosomal protein
YJL178C	0.0325692	RPN4	YJL178C|ATG27|S000003714|Type I membrane protein involved in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; may be involved in membrane delivery to the pre-autophagosomal structure; binds phosphatidylinositol 3-phosphate
YDR213W	0.0325458	RPN4	YDR213W|UPC2|S000002621|Sterol regulatory element binding protein, induces transcription of sterol transport and biosynthetic genes; involved in the anaerobic induction of DAN/TIR mannoproteins and seripauperins; binucleate zinc cluster protein; Ecm22p homolog
YOL103W	0.0323463	RPN4	YOL103W|ITR2|S000005463|Myo-inositol transporter with strong similarity to the major myo-inositol transporter Itr1p, member of the sugar transporter superfamily; expressed constitutively
YJL100W	0.0322725	RPN4	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
YPL190C	0.0320644	RPN4	YPL190C|NAB3|S000006111|Single stranded RNA binding protein; acidic ribonucleoprotein; required for termination of non-poly(A) transcripts and efficient splicing; interacts with Nrd1p
YBR206W	0.0320595	RPN4	YBR206W||S000000410|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene KTR3
YLR437C	0.0315966	RPN4	YLR437C||S000004429|Putative protein of unknown function; epitope tagged protein localizes to the cytoplasm
YGR070W	0.0314937	RPN4	YGR070W|ROM1|S000003302|GDP/GTP exchange protein (GEP) for Rho1p; mutations are synthetically lethal with mutations in rom2, which also encodes a GEP
YGL079W	0.0312209	RPN4	YGL079W||S000003047|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endosome; identified as a transcriptional activator in a high-throughput yeast one-hybrid assay
YMR011W	0.0312165	RPN4	YMR011W|HXT2|S000004613|High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose
YBR170C	0.0309506	RPN4	YBR170C|NPL4|S000000374|Endoplasmic reticulum and nuclear membrane protein, forms a complex with Cdc48p and Ufd1p that recognizes ubiquitinated proteins in the endoplasmic reticulum and delivers them to the proteasome for degradation
YBR111W-A	0.0307017	RPN4	YBR111W-A|SUS1|S000028510|Protein involved in mRNA export coupled transcription activation; component of the SAGA histone acetylase complex
YIL013C	0.0306644	RPN4	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
YDR172W	0.0304829	RPN4	YDR172W|SUP35|S000002579|Translation termination factor eRF3; altered protein conformation creates the [PSI(+)] prion, a dominant cytoplasmically inherited protein aggregate that alters translational fidelity and creates a nonsense suppressor phenotype
YCR015C	0.0303139	RPN4	YCR015C||S000000608|Putative protein of unknown function; YCR015C is not an essential gene
YKL099C	0.0303103	RPN4	YKL099C|UTP11|S000001582|Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA
YHL046C	0.0301385	RPN4	YHL046C|PAU13|S000001038|Putative protein of unknown function; not an essential gene
YDR215C	0.030024	RPN4	YDR215C||S000002623|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; null mutant displays elevated sensitivity to expression of a mutant huntingtin fragment or of alpha-synuclein
YPL160W	0.0296026	RPN4	YPL160W|CDC60|S000006081|Cytosolic leucyl tRNA synthetase, ligates leucine to the appropriate tRNA
YMR044W	0.0291887	RPN4	YMR044W|IOC4|S000004647|Member of a complex (Isw1b) with Isw1p and Ioc2p that exhibits nucleosome-stimulated ATPase activity and acts within coding regions to coordinate transcription elongation with termination and processing, contains a PWWP motif
YOL158C	0.0285107	RPN4	YOL158C|ENB1|S000005518|Endosomal ferric enterobactin transporter, expressed under conditions of iron deprivation; member of the major facilitator superfamily; expression is regulated by Rcs1p and affected by chloroquine treatment
YOL055C	0.0281568	RPN4	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
YPL100W	0.0278802	RPN4	YPL100W|ATG21|S000006021|Phosphoinositide binding protein required for vesicle formation in the cytoplasm-to-vacuole targeting (Cvt) pathway; binds both phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol 3-phosphate; WD-40 repeat protein
YJL223C	0.0277446	RPN4	YJL223C|PAU1|S000003759|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
YLR095C	0.0277309	RPN4	YLR095C|IOC2|S000004085|Member of a complex (Isw1b) with Isw1p and Ioc4p that exhibits nucleosome-stimulated ATPase activity and acts within coding regions to coordinate transcription elongation with termination and processing, contains a PHD finger motif
YGL106W	0.0266704	RPN4	YGL106W|MLC1|S000003074|Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition
YPL011C	0.0263345	RPN4	YPL011C|TAF3|S000005932|TFIID subunit (47 kDa), involved in promoter binding and RNA polymerase II transcription initiation
YMR284W	0.0259587	RPN4	YMR284W|YKU70|S000004897|Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair
YOR042W	0.0258405	RPN4	YOR042W|CUE5|S000005568|Protein containing a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitination; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YML035C	0.0252117	RPN4	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
YER183C	0.0248499	RPN4	YER183C|FAU1|S000000985|5,10-methenyltetrahydrofolate synthetase, involved in folic acid biosynthesis
YDR042C	0.0245469	RPN4	YDR042C||S000002449|Putative protein of unknown function; expression is increased in ssu72-ts69 mutant
YOR072W-A	0.0243331	RPN4	YOR072W-A||S000028582|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YOR072W; originally identified by fungal homology and RT-PCR
YGL213C	0.0242991	RPN4	YGL213C|SKI8|S000003181|Protein involved in exosome mediated 3' to 5' mRNA degradation and translation inhibition of non-poly(A) mRNAs as well as double-strand break formation during meiotic recombination; required for repressing propagation of dsRNA viruses
YJR010W	0.0242327	RPN4	YJR010W|MET3|S000003771|ATP sulfurylase, catalyzes the primary step of intracellular sulfate activation, essential for assimilatory reduction of sulfate to sulfide, involved in methionine metabolism
YGR180C	0.0240707	RPN4	YGR180C|RNR4|S000003412|Ribonucleotide-diphosphate reductase (RNR), small subunit; the RNR complex catalyzes the rate-limiting step in dNTP synthesis and is regulated by DNA replication and DNA damage checkpoint pathways via localization of the small subunits
YDL240W	0.0237905	RPN4	YDL240W|LRG1|S000002399|Putative GTPase-activating protein (GAP) involved in the Pkc1p-mediated signaling pathway that controls cell wall integrity; appears to specifically regulate 1,3-beta-glucan synthesis
YOR354C	0.0235525	RPN4	YOR354C|MSC6|S000005881|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 in high-throughput studies
YDR037W	0.0235042	RPN4	YDR037W|KRS1|S000002444|Lysyl-tRNA synthetase; also identified as a negative regulator of general control of amino acid biosynthesis
YKL064W	0.0230645	RPN4	YKL064W|MNR2|S000001547|Putative magnesium transporter; has similarity to Alr1p and Alr2p, which mediate influx of Mg2+ and other divalent cations
YMR017W	0.0228093	RPN4	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
YHR153C	0.0227899	RPN4	YHR153C|SPO16|S000001196|Protein of unknown function, required for spore formation
YGR280C	0.0219479	RPN4	YGR280C|PXR1|S000003512|Essential protein involved in rRNA and snoRNA maturation; competes with TLC1 RNA for binding to Est2p, suggesting a role in negative regulation of telomerase; human homolog inhibits telomerase; contains a G-patch RNA interacting domain
YLR199C	0.021831	RPN4	YLR199C|PBA1|S000004189|Protein involved in 20S proteasome assembly; forms a heterodimer with Add66p that binds to proteasome precursors; similar to human PAC1 constituent of the PAC1-PAC2 complex involved in proteasome assembly
YIL156W	0.0215487	RPN4	YIL156W|UBP7|S000001418|Ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YEL058W	0.0215174	RPN4	YEL058W|PCM1|S000000784|Essential N-acetylglucosamine-phosphate mutase; converts GlcNAc-6-P to GlcNAc-1-P, which is a precursor for the biosynthesis of chitin and for the formation of N-glycosylated mannoproteins and glycosylphosphatidylinositol anchors
YOR004W	0.0201598	RPN4	YOR004W|UTP23|S000005530|Essential nucleolar protein that is a component of the SSU (small subunit) processome involved in 40S ribosomal subunit biogenesis; has homology to PINc domain protein Fcf1p, although the PINc domain of Utp23p is not required for function
YML009C	0.0201239	RPN4	YML009C|MRPL39|S000004468|Mitochondrial ribosomal protein of the large subunit
YJL222W-A	0.0200443	RPN4	YJL222W-A||S000028663|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR158W	0.0199987	RPN4	YBR158W|AMN1|S000000362|Protein required for daughter cell separation, multiple mitotic checkpoints, and chromosome stability; contains 12 degenerate leucine-rich repeat motifs; expression is induced by the Mitotic Exit Network (MEN)
YDR014W-A	0.0198598	RPN4	YDR014W-A|HED1|S000113613|Meiosis-specific protein that down-regulates Rad51p-mediated mitotic recombination when the meiotic recombination machinery is impaired; early meiotic gene, transcribed specifically during meiotic prophase
YGR069W	0.0198458	RPN4	YGR069W||S000003301|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR323C	0.0195761	RPN4	YOR323C|PRO2|S000005850|Gamma-glutamyl phosphate reductase, catalyzes the second step in proline biosynthesis
YMR009W	0.0193597	RPN4	YMR009W|ADI1|S000004611|Acireductone dioxygenease involved in the methionine salvage pathway; ortholog of human MTCBP-1; transcribed with YMR010W and regulated post-transcriptionally by RNase III (Rnt1p) cleavage; ADI1 mRNA is induced in heat shock conditions
YML064C	0.0189961	RPN4	YML064C|TEM1|S000004529|GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis
YGR158C	0.0188823	RPN4	YGR158C|MTR3|S000003390|3'5' exoribonuclease, exosome subunit; nucleolar protein involved in export of mRNA and ribosomal subunits; homologous to the E. coli exonuclease RNase PH
YER042W	0.0188153	RPN4	YER042W|MXR1|S000000844|Peptide methionine sulfoxide reductase, reverses the oxidation of methionine residues; involved in oxidative damage repair, providing resistance to oxidative stress and regulation of lifespan
YKL065C	0.0184458	RPN4	YKL065C|YET1|S000001548|Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein
YGR021W	0.0183779	RPN4	YGR021W||S000003253|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YIL139C	0.0183628	RPN4	YIL139C|REV7|S000001401|Processivity subunit of DNA polymerase zeta, which is involved in DNA repair and translesion synthesis; required for mutagenesis induced by DNA damage
YEL022W	0.0183223	RPN4	YEL022W|GEA2|S000000748|Guanine nucleotide exchange factor for ADP ribosylation factors (ARFs), involved in vesicular transport between the Golgi and ER, Golgi organization, and actin cytoskeleton organization; similar to but not functionally redundant with Gea1p
YMR208W	0.0181975	RPN4	YMR208W|ERG12|S000004821|Mevalonate kinase, acts in the biosynthesis of isoprenoids and sterols, including ergosterol, from mevalonate
YPL120W	0.0181875	RPN4	YPL120W|VPS30|S000006041|Subunit of phosphatidylinositol (PtdIns) 3-kinase complexes I and II; Complex I is essential in autophagy and Complex II is required for vacuolar protein sorting; ortholog of the higher eukaryotic gene Beclin 1
YMR316C-A	0.0180155	RPN4	YMR316C-A||S000004933|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified gene DIA1/YMR316W
YDR503C	0.0179156	RPN4	YDR503C|LPP1|S000002911|Lipid phosphate phosphatase, catalyzes Mg(2+)-independent dephosphorylation of phosphatidic acid (PA), lysophosphatidic acid, and diacylglycerol pyrophosphate; involved in control of the cellular levels of phosphatidylinositol and PA
YHL017W	0.0175569	RPN4	YHL017W||S000001009|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein co-localizes with clathrin-coated vesicles
YGR093W	0.0174356	RPN4	YGR093W|DRN1|S000003325|Putative debranching enzyme associated ribonuclease; green fluorescent protein (GFP)-fusion protein localizes to the nucleus
YOR237W	0.0173796	RPN4	YOR237W|HES1|S000005763|Protein implicated in the regulation of ergosterol biosynthesis; one of a seven member gene family with a common essential function and non-essential unique functions; similar to human oxysterol binding protein (OSBP)
YGL141W	0.0173244	RPN4	YGL141W|HUL5|S000003109|Ubiquitin-conjugating enzyme (E4), elongates polyubiquitin chains on substrate proteins; works in opposition to Ubp6p polyubiquitin-shortening activity; required for retrograde transport of misfolded proteins into cytoplasm during ERAD
YML003W	0.0173122	RPN4	YML003W||S000004462|Putative protein of unknown function
YGL238W	0.0171723	RPN4	YGL238W|CSE1|S000003207|Nuclear envelope protein that mediates the nuclear export of importin alpha (Srp1p), homolog of metazoan CAS protein, required for accurate chromosome segregation
YBL093C	0.0170482	RPN4	YBL093C|ROX3|S000000189|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme
YEL050C	0.0168592	RPN4	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
YPL034W	0.01624	RPN4	YPL034W||S000005955|Putative protein of unknown function; YPL034W is not essential gene
YKR001C	0.0161583	RPN4	YKR001C|VPS1|S000001709|Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis
YMR153W	0.0159542	RPN4	YMR153W|NUP53|S000004762|Subunit of the nuclear pore complex (NPC), interacts with karyopherin Kap121p or with Nup170p via overlapping regions of Nup53p, involved in activation of the spindle checkpoint mediated by the Mad1p-Mad2p complex
YNR072W	0.0157616	RPN4	YNR072W|HXT17|S000005355|Hexose transporter, up-regulated in media containing raffinose and galactose at pH 7.7 versus pH 4.7, repressed by high levels of glucose
YNR070W	0.0155894	RPN4	YNR070W||S000005353|Putative transporter of the ATP-binding cassette (ABC) family, implicated in pleiotropic drug resistance; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL193W	0.0155572	RPN4	YNL193W||S000005137|Putative protein of unknown function; exhibits a two-hybrid interaction with Yhr151cp in a large-scale analysis
YLR227C	0.015348	RPN4	YLR227C|ADY4|S000004217|Structural component of the meiotic outer plaque, which is a membrane-organizing center that assembles on the cytoplasmic face of the spindle pole body during meiosis II and triggers the formation of the prospore membrane
YBR055C	0.0153326	RPN4	YBR055C|PRP6|S000000259|Splicing factor, component of the U4/U6-U5 snRNP complex
YHR200W	0.0148247	RPN4	YHR200W|RPN10|S000001243|Non-ATPase base subunit of the 19S regulatory particle (RP) of the 26S proteasome; N-terminus plays a role in maintaining the structural integrity of the RP; binds selectively to polyubiquitin chains; homolog of the mammalian S5a protein
YFR050C	0.0147681	RPN4	YFR050C|PRE4|S000001946|Beta 7 subunit of the 20S proteasome
YIR019C	0.0146727	RPN4	YIR019C|MUC1|S000001458|GPI-anchored cell surface glycoprotein (flocculin) required for pseudohyphal formation, invasive growth, flocculation, and biofilms; transcriptionally regulated by the MAPK pathway (via Ste12p and Tec1p) and the cAMP pathway (via Flo8p)
YHR139C-A	0.0145911	RPN4	YHR139C-A||S000003533|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR438W	0.0145028	RPN4	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
YDR527W	0.014338	RPN4	YDR527W|RBA50|S000002935|Protein involved in transcription; interacts with RNA polymerase II subunits Rpb2p, Rpb3, and Rpb11p; has similarity to human RPAP1
YIL094C	0.0141799	RPN4	YIL094C|LYS12|S000001356|Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate
YBR024W	0.0136081	RPN4	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
YOR041C	0.0134712	RPN4	YOR041C||S000005567|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 85% of ORF overlaps the uncharacterized gene CUE5; deletion in cyr1 mutant results in loss of stress resistance
YGR269W	0.0134413	RPN4	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
YOL093W	0.0131478	RPN4	YOL093W|TRM10|S000005453|tRNA methyltransferase, methylates the N-1 position of guanosine in tRNAs
YDL061C	0.0129137	RPN4	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
YER048C	0.0128443	RPN4	YER048C|CAJ1|S000000850|Nuclear type II J heat shock protein of the E. coli dnaJ family, contains a leucine zipper-like motif, binds to non-native substrates for presentation to Ssa3p, may function during protein translocation, assembly and disassembly
YML027W	0.012744	RPN4	YML027W|YOX1|S000004489|Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase; expression is cell cycle-regulated; potential Cdc28p substrate
YMR082C	0.0124061	RPN4	YMR082C||S000004687|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJR114W	0.0122841	RPN4	YJR114W||S000003875|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RSM7/YJR113C
YPR016W-A	0.0122424	RPN4	YPR016W-A||S000007630|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR402W	0.0121341	RPN4	YLR402W||S000004394|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL028W	0.0121282	RPN4	YIL028W||S000001290|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR427W	0.0120195	RPN4	YDR427W|RPN9|S000002835|Non-ATPase regulatory subunit of the 26S proteasome, has similarity to putative proteasomal subunits in other species; null mutant is temperature sensitive and exhibits cell cycle and proteasome assembly defects
YJL173C	0.0119246	RPN4	YJL173C|RFA3|S000003709|Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination
YBR207W	0.0119146	RPN4	YBR207W|FTH1|S000000411|Putative high affinity iron transporter involved in transport of intravacuolar stores of iron; forms complex with Fet5p; expression is regulated by iron; proposed to play indirect role in endocytosis
YDL227C	0.0117305	RPN4	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
YLR055C	0.0117158	RPN4	YLR055C|SPT8|S000004045|Subunit of the SAGA transcriptional regulatory complex but not present in SAGA-like complex SLIK/SALSA, required for SAGA-mediated inhibition at some promoters
YML028W	0.011676	RPN4	YML028W|TSA1|S000004490|Thioredoxin peroxidase, acts as both a ribosome-associated and free cytoplasmic antioxidant; self-associates to form a high-molecular weight chaperone complex under oxidative stress; deletion results in mutator phenotype
YHL019W-A	0.011415	RPN4	YHL019W-A||S000028772|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene APM2/YHL019C
YKR041W	0.0113522	RPN4	YKR041W||S000001749|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YLR120C	0.0113198	RPN4	YLR120C|YPS1|S000004110|Aspartic protease, attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor
YOR202W	0.011262	RPN4	YOR202W|HIS3|S000005728|Imidazoleglycerol-phosphate dehydratase, catalyzes the sixth step in histidine biosynthesis; mutations cause histidine auxotrophy and sensitivity to Cu, Co, and Ni salts; transcription is regulated by general amino acid control via Gcn4p
YFR040W	0.0110341	RPN4	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
YEL029C	0.0109572	RPN4	YEL029C|BUD16|S000000755|Putative pyridoxal kinase, key enzyme in vitamin B6 metabolism; involved in maintaining levels of pyridoxal 5'-phosphate, the active form of vitamin B6; required for genome integrity; homolog of E. coli PdxK; involved in bud-site selection
YML091C	0.0109045	RPN4	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
YOR372C	0.0106134	RPN4	YOR372C|NDD1|S000005899|Transcriptional activator essential for nuclear division; localized to the nucleus; essential component of the mechanism that activates the expression of a set of late-S-phase-specific genes
YKL052C	0.0103506	RPN4	YKL052C|ASK1|S000001535|Essential subunit of the Dam1 complex (aka DASH complex), couples kinetochores to the force produced by MT depolymerization thereby aiding in chromosome segregation; phosphorylated during the cell cycle by cyclin-dependent kinases
YGL248W	0.00998371	RPN4	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
YDL171C	0.00995779	RPN4	YDL171C|GLT1|S000002330|NAD(+)-dependent glutamate synthase (GOGAT), synthesizes glutamate from glutamine and alpha-ketoglutarate; with Gln1p, forms the secondary pathway for glutamate biosynthesis from ammonia; expression regulated by nitrogen source
YER007C-A	0.00986668	RPN4	YER007C-A|TMA20|S000002957|Protein of unknown function that associates with ribosomes and has a putative RNA binding domain; interacts with Tma22p; null mutant exhibits translation defects; has homology to human oncogene MCT-1
YLR005W	0.00983318	RPN4	YLR005W|SSL1|S000003995|Component of the core form of RNA polymerase transcription factor TFIIH, which has both protein kinase and DNA-dependent ATPase/helicase activities and is essential for transcription and nucleotide excision repair; interacts with Tfb4p
YNL044W	0.00957798	RPN4	YNL044W|YIP3|S000004989|Protein localized to COPII vesicles, proposed to be involved in ER to Golgi transport; interacts with members of the Rab GTPase family and Yip1p; also interacts with Rtn1p
YMR308C	0.00950949	RPN4	YMR308C|PSE1|S000004925|Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p
YBR255C-A	0.00928207	RPN4	YBR255C-A||S000007649|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YDL041W	0.00921871	RPN4	YDL041W||S000002199|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene SIR2/YDL042C
YMR314W	0.00919858	RPN4	YMR314W|PRE5|S000004931|Alpha 6 subunit of the 20S proteasome
YBL060W	0.00900157	RPN4	YBL060W|YEL1|S000000156|Guanine nucleotide exchange factor specific for Arf3p; localized to the bud neck and tip; required for localization of Arf3p to the bud neck and tip
YCR006C	0.0083934	RPN4	YCR006C||S000000599|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL303W	0.00801173	RPN4	YNL303W||S000005247|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL130W	0.00788871	RPN4	YGL130W|CEG1|S000003098|Alpha (guanylyltransferase) subunit of the mRNA capping enzyme, a heterodimer (the other subunit is CET1, an RNA 5'-triphophatase) involved in adding the 5' cap to mRNA; the mammalian enzyme is a single bifunctional polypeptide
YHR052W	0.0075858	RPN4	YHR052W|CIC1|S000001094|Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles
YGR094W	0.00740938	RPN4	YGR094W|VAS1|S000003326|Mitochondrial and cytoplasmic valyl-tRNA synthetase
YBR186W	0.00734222	RPN4	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
YKL071W	0.00724308	RPN4	YKL071W||S000001554|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YBR152W	0.00723033	RPN4	YBR152W|SPP381|S000000356|mRNA splicing factor, component of U4/U6.U5 tri-snRNP; interacts genetically and physically with Prp38p
YLR097C	0.00722036	RPN4	YLR097C|HRT3|S000004087|Putative SCF-ubiquitin ligase F-box protein, based on both genetic and physical interactions and sequence similarity; identified in association with Cdc53p, Skp1p and Ubi4 in large and small-scale studies
YJR138W	0.00686836	RPN4	YJR138W|IML1|S000003899|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane
YLR013W	0.00686356	RPN4	YLR013W|GAT3|S000004003|Protein containing GATA family zinc finger motifs
YDR311W	0.00670371	RPN4	YDR311W|TFB1|S000002719|Subunit of TFIIH and nucleotide excision repair factor 3 complexes, required for nucleotide excision repair, target for transcriptional activators
YDL073W	0.00660193	RPN4	YDL073W||S000002231|Putative protein of unknown function; YDL073W is not an essential gene
YDL071C	0.00644531	RPN4	YDL071C||S000002229|Hypothetical protein
YEL071W	0.00634355	RPN4	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
YGR121W-A	0.00622414	RPN4	YGR121W-A||S000028550|Putative protein of unknown function
YHR012W	0.00620287	RPN4	YHR012W|VPS29|S000001054|Endosomal protein that is a subunit of the membrane-associated retromer complex essential for endosome-to-Golgi retrograde transport; forms a subcomplex with Vps35p and Vps26p that selects cargo proteins for endosome-to-Golgi retrieval
YDR234W	0.00605222	RPN4	YDR234W|LYS4|S000002642|Homoaconitase, catalyzes the conversion of homocitrate to homoisocitrate, which is a step in the lysine biosynthesis pathway
YAL047C	0.0060293	RPN4	YAL047C|SPC72|S000000045|Component of the cytoplasmic Tub4p (gamma-tubulin) complex, binds spindle pole bodies and links them to microtubules; has roles in astral microtubule formation and stabilization
YDR171W	0.00588699	RPN4	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
YNL335W	0.00571204	RPN4	YNL335W|DDI3|S000005279|Hypothetical protein
YMR290W-A	0.00552691	RPN4	YMR290W-A||S000004904|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps 5' end of essential HAS1 gene which encodes an ATP-dependent RNA helicase
YCR093W	0.00537333	RPN4	YCR093W|CDC39|S000000689|Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation; basal transcription factor
YGR266W	0.00518223	RPN4	YGR266W||S000003498|Protein of unknown function, predicted to contain a single transmembrane domain; localized to both the mitochondrial outer membrane and the plasma membrane
YOR201C	0.00517728	RPN4	YOR201C|MRM1|S000005727|Ribose methyltransferase that modifies a functionally critical, conserved nucleotide in mitochondrial 21S rRNA
YGL117W	0.00515477	RPN4	YGL117W||S000003085|Putative protein of unknown function
YLR009W	0.00512952	RPN4	YLR009W|RLP24|S000003999|Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis
YDL060W	0.00495488	RPN4	YDL060W|TSR1|S000002218|Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles
YPR016C	0.00488481	RPN4	YPR016C|TIF6|S000006220|Constituent of 66S pre-ribosomal particles, has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits
YHL038C	0.00478009	RPN4	YHL038C|CBP2|S000001030|Mitochondrial protein required for splicing of the group I intron aI5 of the COB pre-mRNA, binds to the RNA to promote splicing; also involved in but not essential for splicing of the COB bI2 intron and the intron in the 21S rRNA gene
YJL144W	0.00470073	RPN4	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
YGL092W	0.00449029	RPN4	YGL092W|NUP145|S000003060|Essential nucleoporin, catalyzes its own cleavage in vivo to generate a C-terminal fragment that assembles into the Nup84p subcomplex of the nuclear pore complex, and an N-terminal fragment of unknown function that is homologous to Nup100p
YGR181W	0.0042778	RPN4	YGR181W|TIM13|S000003413|Mitochondrial intermembrane space protein, forms a complex with TIm8p that mediates import and insertion of a subset of polytopic inner membrane proteins; may prevent aggregation of incoming proteins in a chaperone-like manner
YKR040C	0.00410158	RPN4	YKR040C||S000001748|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YKR041W
YML004C	0.00389219	RPN4	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
YOR353C	0.00360106	RPN4	YOR353C|SOG2|S000005880|Key component of the RAM signaling network, required for proper cell morphogenesis and cell separation after mitosis
YGR250C	0.00354397	RPN4	YGR250C||S000003482|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR060W	0.00353691	RPN4	YDR060W|MAK21|S000002467|Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein
YPL185W	0.00279015	RPN4	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
YBR120C	0.00274422	RPN4	YBR120C|CBP6|S000000324|Mitochondrial translational activator of the COB mRNA; phosphorylated
YJL161W	0.00265273	RPN4	YJL161W|FMP33|S000003697|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR088C	0.00250461	RPN4	YDR088C|SLU7|S000002495|RNA splicing factor, required for ATP-independent portion of 2nd catalytic step of spliceosomal RNA splicing; interacts with Prp18p; contains zinc knuckle domain
YMR196W	0.00233957	RPN4	YMR196W||S000004809|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR196W is not an essential gene
YAL043C	0.00227978	RPN4	YAL043C|PTA1|S000000041|Subunit of holo-CPF, a multiprotein complex and functional homolog of mammalian CPSF, required for the cleavage and polyadenylation of mRNA and snoRNA 3' ends; involved in pre-tRNA processing; binds to the phosphorylated CTD of RNAPII
YPR119W	0.00225925	RPN4	YPR119W|CLB2|S000006323|B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome
YDR305C	0.00215681	RPN4	YDR305C|HNT2|S000002713|Dinucleoside triphosphate hydrolase; has similarity to the tumor suppressor FHIT and belongs to the histidine triad (HIT) superfamily of nucleotide-binding proteins
YKL135C	0.00188656	RPN4	YKL135C|APL2|S000001618|Beta-adaptin, large subunit of the clathrin-associated protein (AP-1) complex; binds clathrin; involved in clathrin-dependent Golgi protein sorting
YNL042W	0.00165167	RPN4	YNL042W|BOP3|S000004987|Protein of unknown function, potential Cdc28p substrate; overproduction suppresses a pam1 slv3 double null mutation and confers resistance to methylmercury
YDR150W	0.0013428	RPN4	YDR150W|NUM1|S000002557|Protein required for nuclear migration, localizes to the mother cell cortex and the bud tip; may mediate interactions of dynein and cytoplasmic microtubules with the cell cortex
YEL049W	0.00091899	RPN4	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
YGR222W	0.000653552	RPN4	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
YMR303C	0.000270665	RPN4	YMR303C|ADH2|S000004918|Glucose-repressible alcohol dehydrogenase II, catalyzes the conversion of ethanol to acetaldehyde; involved in the production of certain carboxylate esters; regulated by ADR1
YOR338W	0.000153356	RPN4	YOR338W||S000005865|Putative protein of unknown function; YOR338W transcription is regulated by Azf1p and its transcript is a specific target of the G protein effector Scp160p; identified as being required for sporulation in a high-throughput mutant screen
