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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