Table 2

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

* Genes in bold indicate their encoding proteins or enzymes are involved in more than one function

Ma and Liu BMC Genomics 2010 11:660   doi:10.1186/1471-2164-11-660