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Table 2 Gene Ontology (GO) categories and terms for significantly induced genes by HMF during the lag phase in Saccharomyces cerevisiae

From: Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

GO ID GO term Gene(s)
Cellular component
GO:0005737 Cytoplasm SHP1*, ATG8, YBL107C, HSP26, NPL4, CHA1, GPM2, SNQ2, RPN9, SLF1, SSA4, OTU1, RPN12, PYC1, ARI1, YGR111W, ECM29, PUT2, PRE3, MET3, MET14, TPO1, ALT1, PUT1, YAP1, PGA3, ERO1, YNL155W, PRE6, GRE2, SGT2, RSB1, YOR059C, PDR5, TPO4, PRE10, ALD4, CAR1
GO:0005634 Nucleus SHP1, YBL100W-A, HSP26, RAD16, RPT2, RPN4, YDR210W-B, YDR316W-B, YDR365W-B, PRE1, SSA4, MAG1, OTU1, ARI1, YGR111W, ECM29, YKR011C, YAP1, YNL155W, GRE2, YOR052C, RPT4
GO:0016020 Membrane ATG8, NPL4, SNQ2, PDR15, DDI1, YOR1, TPO1, PGA3, RSB1, PDR5, TPO4, MCH5, PDR12, PRM4
GO:0005575 Cellular component unknown IMD1, YBR062C, YBR255C-A, YDR034W-B, YER137C, YGR035C, YHR138C , YLL056C, ICT1, OYE3
GO:0005886 Plasma membrane SNQ2, DDI1, YOR1, TPO1, PGA3, RSB1, PDR5, TPO4, MCH5, PDR12
GO:0005739 Mitochondrion CHA1, SNQ2, PUT2, MET3, ALT1, PUT1, PRE6, PDR5, ALD4
GO:0005783 Endoplasmic reticulum NPL4, PGA3, ERO1, RSB1
GO:0005773 Vacuole ATG8, TPO1, TPO4
GO:0005624 Membrane fraction SNQ2, YOR1
GO:0005933 Cellular bud TPO1
GO:0005618 Cell wall TIR4
GO:0012505 Endomembrane system NPL4
GO:0030427 Cite of polarized growth CAR1
Other Other PRE7, ADH7, RPT3, PUP3
Biological process
GO:0008150 Biological process unknown IMD1, YBL107C, YBR062C, YBR255C-A, GPM2, YDR034W-B, YER137C, ARI1 , YGR035C, YKR011C, YLL056C, YNL155W , TIR4, YOR052C, YOR059C, PRM4, OYE3
GO:0044257 Cellular protein catabolic process PRE7, SHP1, RAD16, NPL4, RPT2, RPT3, RPN9, PRE1, PUP3, DDI1, RPN12, PRE3, PRE6, RPT4, PRE10
GO:0006810 Transport ATG8, PDR15, SSA4, DDI1, YOR1, TPO1, PGA3, RSB1, PDR5, TPO4, MCH5, PDR12
GO:0006950 Response to stress ATG8, HSP26, RAD16, RPN4, SNQ2, PRE1, SSA4, MAG1, PRE3, YAP1, SGT2
GO:0042221 Response to chemical stimulus RPN4, SNQ2, PDR15, YOR1, MET14, YAP1, PDR5
GO:0006519 Cellular amino acid and derivative metabolic process CHA1, PUT2, MET3, MET14, ALT1, PUT1, CAR1
GO:0032196 Transposition YBL100W-A, YDR210W-B, YDR316W-B, YDR365W-B
GO:0006457 Protein folding HSP26, SSA4, ERO1
GO:0006350 Transcription RPN4, OTU1, YAP1
GO:0006464 Protein modification process RAD16, OTU1, ERO1
GO:0030435 Sporulation resulting in formation of a cellular spore SHP1, PRE1, PRE3
GO:0006259 DNA metabolic process RAD16, RPN4, MAG1
GO:0016044 Membrane organization ATG8, YHR138C, RSB1
GO:0007033 Vacuole organization ATG8, YHR138C
GO:0044262 Cellular carbohydrate metabolic process SHP1, PYC1
GO:0044255 Cellular lipid metabolic process ICT1, GRE2
GO:0006766 Vitamin metabolic process PYC1, ALD4
GO:0046483 Heterocycle metabolic process PUT2, PUT1
GO:0051186 Cofactor metabolic process PYC1, ALD4
GO:0016192 Vesicle-mediated transport ATG8, DDI1
GO:0051276 Chromosome organization RAD16
GO:0016070 RNA metabolic process YAP1
GO:0006412 Translation SLF1
GO:0006091 Generation of precursor metabolites and energy SHP1
GO:0070271 Protein complex biogenesis RPN9
GO:0007049 Cell cycle RPN4
GO:0019725 Cellular homeostasis SLF1
Other Other ADH7, YGR111W , ECM29
Molecular function
GO:0016787 Hydrolase activity PRE7, RAD16, RPT2, SNQ2, YDR210W-B, YDR316W-B, YDR365W-B, RPT3, PDR15, PRE1, PUP3, SSA4, MAG1, OTU1, RPN12, YOR1, PRE3, PRE6, RSB1, PDR5, RPT4, PRE10, PDR12, CAR1
GO:0003674 Molecular function unknown IMD1, ATG8 , YBL107C, YBR062C, NPL4 , YBR255C-A, GPM2, YDR034W-B, YER137C, YGR035C, YGR111W , YKR011C, YLL056C, PGA3 , YNL155W , SGT2, TIR4, YOR052C, YOR059C, PRM4
GO:0008233 Peptidase activity PRE7, RPT2, YDR210W-B, YDR316W-B, YDR365W-B, RPT3, PRE1, PUP3, OTU1, RPN12, PRE3, PRE6, RPT4, PRE10
GO:0005215 Transporter activity SNQ2, PDR15, YOR1, TPO1, RSB1, PDR5, TPO4, MCH5, PDR12
GO:0016491 Oxidoreductase activity ADH7, ARI1 , PUT2 , PUT1 , ERO1 , GRE2 , ALD4 , OYE3
GO:0005515 Protein binding YBL100W-A, HSP26, YDR210W-B, YDR316W-B, YDR365W-B, SSA4, DDI1, ECM29
GO:0016740 Transferase activity YDR210W-B, YDR316W-B, YDR365W-B, MET3, MET14, ALT1, ICT1
GO:0003723 RNA binding YBL100W-A, YDR210W-B, YDR316W-B, YDR365W-B, SLF1
GO:0016779 Nucleotidyltransferase activity YDR210W-B, YDR316W-B, YDR365W-B, MET3
GO:0003677 DNA binding RAD16, RPN4, YAP1
GO:0016874 Ligase activity RAD16, PYC1
GO:0030528 Transcription regulator activity RPN4, YAP1
GO:0030234 Enzyme regulator activity SHP1, YHR138C
GO:0016829 Lyase activity CHA1
GO:0005198 Structural molecule activity RPN9
GO:0016853 Isomerase activity GPM2
  1. * Genes in bold indicate their encoding proteins or enzymes are involved in more than one function