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Table 3 Differentially expressed and annotated genes in the Δ aft1 vs. control (wild type) strain

From: Pichia pastoris Aft1 - a novel transcription factor, enhancing recombinant protein secretion

Up-regulated genes (Δaft1vs. control)
GO slim term - Biological process Number (Genes)
GO:0006811 ion transport 7 ( AQR1 ATX1 GEF1 MEP2 TPO3 YHL008C ZRT1 )
GO:0008150 biological_process* 6 ( ECM13 GPM3 YEL023C YLR156C-A YLR278C YOR292C )
GO:0055085 transmembrane transport 6 ( AQR1 GEF1 MEP2 STL1 TPO3 ZRT1 )
GO:0006366 transcription from RNA polymerase II promoter 5 ( GCR1 PHD1 RPM2 UGA3 YLR278C )
GO:0042221 response to chemical 5 ( AQR1 ATX1 GCR1 SLI1 UGA3 )
GO:0006520 cellular amino acid metabolic process 4 ( ADH2 ECM4 SFA1 UGA3 )
GO:0007124 pseudohyphal growth 4 ( HMS1 MEP2 PHD1 PTP1 )
GO:0051186 cofactor metabolic process 4 ( ADH2 ALD4 BIO2 THI21 )
GO:0005975 carbohydrate metabolic process 3 ( DOG1 GCR1 GPM3 )
GO:0006091 generation of precursor metabolites and energy 2 ( GCR1 GPM3 )
GO:0006766 vitamin metabolic process 2 ( BIO2 THI21 )
GO:0006873 cellular ion homeostasis 2 ( ATX1 GEF1 )
GO:0055086 nucleobase-containing small molecule metabolic process 2 ( ADH2 ALD4 )
GO:0001403 invasive growth in response to glucose limitation 1 ( PTP1 )
GO:0002181 cytoplasmic translation 1 ( RPM2 )
GO:0006325 chromatin organization 1 ( GCR1 )
GO:0006397 mRNA processing 1 ( RPM2 )
GO:0006470 protein dephosphorylation 1 ( PTP1 )
GO:0006629 lipid metabolic process 1 ( YJU3 )
GO:0006865 amino acid transport 1 ( AQR 1 )
GO:0006979 response to oxidative stress 1 ( ATX1 )
GO:0007005 mitochondrion organization 1 ( RPM2 )
GO:0008033 tRNA processing 1 ( RPM2 )
GO:0008643 carbohydrate transport 1 ( STL1 )
GO:0070647 protein modification by small protein conjugation or removal 1 ( PCI8 )
Down-regulated genes (Δ aft1 vs. control)
GO slim term - Biological process Number (Genes)
GO:0006811 ion transport 4 ( ATO2 JEN1 TAT2 VMA8 )
GO:0055085 transmembrane transport 4 ( ITR1 JEN1 PEX13 TAT2 )
GO:0006281 DNA repair 3 ( PCD1 RVB1 YRA1 )
GO:0006325 chromatin organization 3 ( ACS1 RLF2 RVB1 )
GO:0006366 transcription from RNA polymerase II promoter 3 ( MIG1 RVB1 YHP1 )
GO:0006974 cellular response to DNA damage stimulus 3 ( PCD1 RVB1 YRA1 )
GO:0008150 biological_process* 3 ( NBA1 TOS8 YHR177W )
GO:0005975 carbohydrate metabolic process 2 ( CTS1 MIG1 )
GO:0006766 vitamin metabolic process 2 ( SNO1 SNZ3 )
GO:0051186 cofactor metabolic process 2 ( ACS1 SNZ3 )
GO:0055086 nucleobase-containing small molecule metabolic process 2 ( PCD1 YRA1 )
GO:0070271 protein complex biogenesis 2 ( PEX13 RLF2 )
GO:0000278 mitotic cell cycle 1 ( YHP1 )
GO:0000910 cytokinesis 1 ( CTS1 )
GO:0002181 cytoplasmic translation 1 ( RPL4A )
GO:0006091 generation of precursor metabolites and energy 1 ( ACS1 )
GO:0006520 cellular amino acid metabolic process 1 ( SNO1 )
GO:0006605 protein targeting 1 ( PEX13 )
GO:0006865 amino acid transport 1 ( TAT2 )
GO:0006873 cellular ion homeostasis 1 ( VMA8 )
GO:0007031 peroxisome organization 1 ( PEX13 )
GO:0008643 carbohydrate transport 1 ( JEN1 )
GO:0015931 nucleobase-containing compound transport 1 ( YRA1 )
GO:0016570 histone modification 1 ( ACS1 )
GO:0018193 peptidyl-amino acid modification 1 ( ACS1 )
GO:0042221 response to chemical 1 ( MIG1 )
GO:0042594 response to starvation 1 ( MIG1 )
GO:0043543 protein acylation 1 ( ACS1 )
GO:0048193 Golgi vesicle transport 1 ( BRE5 )
GO:0051049 regulation of transport 1 ( BRE5 )
GO:0051169 nuclear transport 1 ( YRA1 )
GO:0070647 protein modification by small protein conjugation or removal 1 ( BRE5 )
  1. *Biological process is unkown.
  2. Genes were categorized into biological function GO terms using AmiGO GO Slimmer (Yeast GO slim set, [25]).