Spreadsheet: 2ac9e15f-53cc-4e94-b605-26a6edeb0d97
Sheet: Sheet1

Table S8:  Genes with RTE < 0.45; the table includes the ORF, name, RTE, and description of each gene. Genes that are related to regulation are marked in blue. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6
GO enrichments according to SGD for this group of genes appear below.
ORF | Name | RTE
YFL004W | VTC2 | 0.391206 | Vacuolar membrane protein involved in vacuolar polyphosphate accumulation; functions as a regulator of vacuolar H+-ATPase activity and vacuolar transporter chaperones; involved in protein localization and non-autophagic vacuolar fusion
YGR234W | YHB1 | 0.303549 | Nitric oxide oxidoreductase, flavohemoglobin involved in nitric oxide detoxification; plays a role in the oxidative and nitrosative stress responses
[NAME] | STE4 | 0.43952 | G protein beta subunit, forms a dimer with Ste18p to activate the mating signaling pathway, forms a heterotrimer with Gpa1p and Ste18p to dampen signaling; may recruit Rho1p to the polarized growth site during mating; contains WD40 repeats
YJL033W | HCA4 | 0.424548 | Putative nucleolar DEAD box [NAME] helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis
YMR276W | DSK2 | 0.448755 | Nuclear-enriched ubiquitin-like polyubiquitin-binding protein, required for spindle pole body (SPB) duplication and for transit through the G2/M phase of the cell cycle, involved in proteolysis, interacts with the proteasome
YOL057W | non | 0.428985 | Putative metalloprotease
YBR023C | CHS3 | 0.433769 | 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
YOR153W | PDR5 | 0.315782 | Short-lived membrane ABC (ATP-binding cassette) transporter, actively exports various drugs, expression regulated by Pdr1p; also involved in steroid transport, cation resistance, and cellular detoxification during exponential growth
YJL001W | PRE3 | 0.307147 | 20S proteasome beta-type subunit, responsible for cleavage after acidic residues in peptides
YGR014W | MSB2 | 0.395569 | Mucin family member at the head of the Cdc42p- and MAP kinase-dependent filamentous growth signaling pathway; also functions as an osmosensor in parallel to the Sho1p-mediated pathway; potential Cdc28p substrate
YPL106C | SSE1 | 0.35824 | ATPase that is a component of the heat shock protein Hsp90 chaperone complex; binds unfolded proteins; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm
YBL068W | PRS4 | 0.443191 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, involved in nucleotide, histidine, and tryptophan biosynthesis; one of a five related enzymes, which are active as heteromultimeric complexes
YPL093W | NOG1 | 0.442577 | Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins
YNL282W | POP3 | 0.312732 | Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursors to generate mature 5' ends
[NAME] | SEC3 | 0.380508 | Non-essential subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, Exo84p) which mediates targeting of post-Golgi vesicles to sites of active exocytosis; Sec3p specifically is a spatial landmark for secretion
YLL034C | RIX7 | 0.418413 | Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions
YDR177W | UBC1 | 0.407254 | Ubiquitin-conjugating enzyme that mediates selective degradation of short-lived and abnormal proteins; plays a role in vesicle biogenesis and ER-associated protein degradation (ERAD); component of the cellular stress response
YOR160W | MTR10 | 0.397217 | Nuclear import receptor, mediates the nuclear localization of proteins involved in mRNA-nucleus export; promotes dissociation of mRNAs from the nucleus-cytoplasm mRNA shuttling protein Npl3p
[NAME] | [NAME] | 0.43407 | Vacuolar membrane zinc transporter, transports zinc from the cytosol into the vacuole for storage; also has a role in resistance to zinc shock resulting from a sudden influx of zinc into the cytoplasm
[NAME] | MNN5 | 0.434974 | Alpha-1,2-mannosyltransferase, responsible for addition of the second alpha-1,2-linked mannose of the branches on the mannan backbone of oligosaccharides, localizes to an early Golgi compartment
YHR200W | RPN10 | 0.342458 | 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
YDL128W | VCX1 | 0.423666 | Vacuolar H+/Ca2+ exchanger involved in control of cytosolic Ca2+ concentration; has similarity to sodium/calcium exchangers, including the bovine Na+/Ca2+,K+ antiporter
YGR281W | YOR1 | 0.305237 | Plasma membrane transporter of the ATP-binding cassette (ABC) family, mediates export of many different organic anions including oligomycin
YBR207W | FTH1 | 0.371388 | 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
YBR162C | TOS1 | 0.39202 | Covalently-bound cell wall protein of unknown function; identified as a cell cycle regulated SBF target gene; deletion mutants are highly resistant to treatment with beta-1,3-glucanase; has sequence similarity to YJL171C
YMR128W | ECM16 | 0.370103 | Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis
YOR207C | [NAME] | 0.441964 | Second-largest subunit of RNA polymerase III, which is responsible for the transcription of tRNA and 5S RNA genes, and other low molecular weight RNAs
YGR128C | UTP8 | 0.393927 | Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA
YDL185W | TFP1 | 0.406126 | binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease
YJR048W | CYC1 | 0.348203 | Cytochrome c, isoform 1; electron carrier of the mitochondrial intermembrane space that transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration
YGR279C | SCW4 | 0.353064 | Cell wall protein with similarity to glucanases; scw4 scw10 double mutants exhibit defects in mating
YBL024W | NCL1 | 0.359983 | S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase, methylates cytosine to m5C at several positions in tRNAs and intron-containing pre-tRNAs; similar to Nop2p and human proliferation associated nucleolar protein p120
[NAME] | PRY1 | 0.436484 | Protein of unknown function, has similarity to Pry2p and Pry3p and to the plant PR-1 class of pathogen related proteins
YEL055C | POL5 | 0.339151 | Protein with sequence similarity to the human MybBP1A and weak sequence similar to B-type DNA polymerases, not required for chromosomal DNA replication; required for the synthesis of rRNA
YOR151C | RPB2 | 0.421908 | RNA polymerase II second largest subunit B150, part of central core; similar to bacterial beta subunit
YDR077W | SED1 | 0.416099 | Major stress-induced structural GPI-cell wall glycoprotein in stationary-phase cells, associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites
YKL068W | NUP100 | 0.393927 | Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor [NAME] and with karyopherin Kap95p; homologous to Nup116p
YPL178W | CBC2 | 0.436484 | Small subunit of the heterodimeric cap binding complex that also contains Sto1p, component of the spliceosomal commitment complex; interacts with Npl3p, possibly to package mRNA for export from the nucleus; contains an RNA-binding motif
YKL164C | PIR1 | 0.217789 | O-glycosylated protein required for cell wall stability; attached to the cell wall via beta-1,3-glucan; mediates mitochondrial translocation of Apn1p; expression regulated by the cell integrity pathway and by Swi5p during the cell cycle
YDR165W | TRM82 | 0.350382 | Subunit of a tRNA methyltransferase complex composed of Trm8p and Trm82p that catalyzes 7-methylguanosine modification of tRNA
[NAME] | FUS3 | 0.368823 | Mitogen-activated protein kinase involved in mating pheromone response; activated by phosphorylation by Ste7p; provides specificity during the mating vs. filamentous growth response by phosphorylating transcriptional and cytoplasmic targets
YMR229C | RRP5 | 0.317318 | Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome
[NAME] | ACC1 | 0.436786 | Acetyl-CoA carboxylase, biotin containing enzyme that catalyzes the carboxylation of acetyl-CoA to form malonyl-CoA; required for de novo biosynthesis of long-chain fatty acids
YCL028W | [NAME] | 0.442577 | [PIN(+)] prion, an infectious protein conformation that is generally an ordered protein aggregate
YBR287W | ZSP1 | 0.293615 | Protein of unknown function; mutation results in a zinc sensitive phenotype
YGR090W | UTP22 | 0.346758 | Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data
YDR461W | MFA1 | 0.292803 | Mating pheromone a-factor, made by a cells; interacts with alpha cells to induce cell cycle arrest and other responses leading to mating; biogenesis involves C-terminal modification, N-terminal proteolysis, and export; also encoded by MFA2
YOR133W | EFT1 | 0.21479 | Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin
YBR067C | TIP1 | 0.310142 | Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat- and cold-shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins
YPL195W | APL5 | 0.099373 | Delta adaptin-like subunit of the clathrin associated protein complex (AP-3); functions in transport of alkaline phosphatase to the vacuole via the alternate pathway, suppressor of loss of casein kinase 1 function
Go enrichments
Process
GOID | GO_term | Cluster frequency | Background frequency | P-value | Gene(s) annotated to the term | Directly Annotated GOID List
16043 | cellular component organization and biogenesis | 31 out of 50 genes, 62.0% | 2186 out of 7288 background genes, 30.0% | 0.00095 | FUS3:NCL1:PRS4:CHS3:TIP1:FTH1:TFP1:SED1:TRM82:UBC1:SEC3:VTC2:MSB2:UTP22:UTP8:YOR1:HCA4:NUP100:PIR1:RIX7:ECM16:RRP5:DSK2:POP3:ACC1:MTR10:STE4:NOG1:SSE1:CBC2:APL5 | 750:30468:398:105:6403:6404:6406:6407:6408:6513:6409:30433:6379:723:30476:7103:42273:6886:7035:6887:6166:2:6998:6999:42493:6810:1402:6633:1403:6457:42026:42787:910:54:55:30488:6207:6893:16192:6314:6896:6897:7047:31684:162:6606:6607:6608:6609:6468:19538:16050:6827:42144:30490:6970:42254:7121:6038:7050:8104:8033:9847:6610:209:6611:6364:6365:6189:6904:6906
42254 | ribosome biogenesis and assembly | 11 out of 50 genes, 22.0% | 330 out of 7288 background genes, 4.5% | 0.00385 | NCL1:PRS4:TRM82:UTP22:UTP8:HCA4:RIX7:ECM16:RRP5:POP3:NOG1 | 105:6379:42273:6166:54:55:6207:30488:162:30490:42254:8033:6364:6365:6189
Component
GOID | GO_term | Cluster frequency | Background frequency | P-value | Gene(s) annotated to the term | Directly Annotated GOID List
44464 | cell part | 50 out of 50 genes, 100.0% | 5496 out of 7288 background genes, 75.4% | 8.66e-05 | FUS3:NCL1:PRS4:CHS3:TIP1:TOS1:[NAME]:ZSP1:[NAME]:VCX1:TFP1:SED1:TRM82:UBC1:MFA1:POL5:SEC3:VTC2:MSB2:UTP22:UTP8:YHB1:SCW4:YOR1:RPN10:PRE3:HCA4:PRY1:MNN5:CYC1:NUP100:PIR1:RIX7:ECM16:RRP5:ZRC1:DSK2:POP3:ACC1:YOL057W:EFT1:RPB2:PDR5:MTR10:[NAME]:STE4:NOG1:SSE1:CBC2:APL5 | 5783:9277:5789:43332:45009:30123:30687:145:5730:324:502:5625:5643:5732:5628:329:5840:5737:5665:5576:5666:5739:5934:5829:5846:5935:5774:5758:5937:5759:5794:5886:19774:5887:131:221:243:5634:172:5635:5655:5834:8540:30427
5623 | cell | 50 out of 50 genes, 100.0% | 5497 out of 7288 background genes, 75.4% | 8.74e-05 | FUS3:NCL1:PRS4:CHS3:TIP1:TOS1:[NAME]:ZSP1:[NAME]:VCX1:TFP1:SED1:TRM82:UBC1:MFA1:POL5:SEC3:VTC2:MSB2:UTP22:UTP8:YHB1:SCW4:YOR1:RPN10:PRE3:HCA4:PRY1:MNN5:CYC1:NUP100:PIR1:RIX7:ECM16:RRP5:ZRC1:DSK2:POP3:ACC1:YOL057W:EFT1:RPB2:PDR5:MTR10:[NAME]:STE4:NOG1:SSE1:CBC2:APL5 | 5783:9277:5789:43332:45009:30123:30687:145:5730:5625:502:324:5643:5732:5628:5840:329:5737:5665:5576:5666:5739:5934:5829:5846:5935:5758:5774:5937:5759:5794:19774:5886:5887:131:221:243:5634:172:5635:5655:5834:8540:30427