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Table 3 Gene ontology analysis of transcriptional responses in host dependence

From: Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis

GO ID Description IW vs CW IC vs CC II vs CI
Up-regulated
GO:0000902 cell morphogenesis   FKS1  
GO:0005975 carbohydrate metabolic process   ALG8, FKS1, GPH1, IMA1, IMA3, KRE6, MAL12, SUC2 CDC19, GPH1, IMA3, KRE6, MAL32, SUC2
GO:0006091 generation of precursor metabolites and energy   CYT1, GPH1 ACS1, CDC19, GPH1
GO:0006325 chromatin organization    ACS1
GO:0006470 protein dephosphorylation   YMR1  
GO:0006486 protein glycosylation   ALG8  
GO:0006520 cellular amino acid metabolic process   ASN1, CPA2, PDC6, URA8, YIL168W ASN1, DYS1, GCV3, GDH2, GDH3, MET16, YIL168W
GO:0006629 lipid metabolic process   ALG8, URA8, YJR107W, YMR1 ERG7, FOX2, MET16
GO:0006766 vitamin metabolic process   BIO2  
GO:0006873 cellular ion homeostasis   SOD1  
GO:0006897 endocytosis   FKS1  
GO:0006979 response to oxidative stress   CTT1, SOD1  
GO:0007005 mitochondrion organization    PPE1
GO:0009311 oligosaccharide metabolic process   ALG8, IMA1, IMA3, MAL12, SUC2 IMA3, MAL32, SUC2
GO:0016570 histone modification    ACS1
GO:0018193 peptidyl-amino acid modification    ACS1, DYS1
GO:0032543 mitochondrial translation    PPE1
GO:0042221 response to chemical stimulus   CTT1, SOD1 MNL1
GO:0043543 protein acylation    ACS1
GO:0045333 cellular respiration   CYT1  
GO:0051049 regulation of transport   FKS1  
GO:0051186 cofactor metabolic process   ACH1, BIO2 ACS1, QNS1
GO:0051603 proteolysis involved in cellular protein catabolic process    MNL1
GO:0055086 nucleobase-containing small molecule metabolic process   ADO1, URA8 QNS1
GO:0070271 protein complex biogenesis    CYC3
GO:0071554 cell wall organization or biogenesis   KRE6, SOD1 KRE6
Un-identified, up-regulated genes*   NIT1 POT1 BDH1 NIT1 POT1
Down-regulated
GO:0000746 conjugation   CHS5  
GO:0000910 cytokinesis    CHS5
GO:0005975 carbohydrate metabolic process CDC19 ALG13, ALG2, CWH41, DOG1, DOG2, FBA1, HXK1, INM1, PYC1, STT3 CHS5, DOG1, DOG2, GAL7, INM1, PGI1, RBK1
GO:0006091 generation of precursor metabolites and energy ACS1, CDC19 COX6, FBA1, HXK1, OLE1 COX6, PGI1, TRX3
GO:0006281 DNA repair   YNK1  
GO:0006325 chromatin organization ACS1   
GO:0006457 protein folding    CPR4
GO:0006486 protein glycosylation   ALG2, CWH41, STT3  
GO:0006520 cellular amino acid metabolic process GCV3, GDH3 CAR2, GLN1, IRC7, LEU1, MET13, PUT2, THR1, TRP5, YGR012W ALT2, LYS9, PUT2, THR1, THR4, YGR012W
GO:0006629 lipid metabolic process   ALG13, ALG2, ECT1, ERG26, ERG4, INM1, IRC7, MET13, NCP1, OLE1, THR1 ARE1, ATG15, ECT1, INM1, MVD1, NCP1, THR1, YAT1
GO:0006974 response to DNA damage stimulus   YNK1  
GO:0006979 response to oxidative stress    TRX3
GO:0008033 tRNA processing   PUS2  
GO:0008643 carbohydrate transport   HXK1  
GO:0009311 oligosaccharide metabolic process   ALG2, CWH41  
GO:0009451 RNA modification   PUS2  
GO:0010324 membrane invagination    ATG15
GO:0016570 histone modification ACS1   
GO:0018193 peptidyl-amino acid modification ACS1   CPR4
GO:0042221 response to chemical stimulus    TRX3
GO:0043543 protein acylation ACS1   
GO:0043934 sporulation    CHS5
GO:0045333 cellular respiration   COX6 COX6
GO:0048193 Golgi vesicle transport    CHS5
GO:0051186 cofactor metabolic process ACS1 HEM2, MET13, NMA2, NPY1, PNC1, PYC1 MVD1, NMA1, NMA2, PGI1
GO:0051603 proteolysis involved in cellular protein catabolic process   ATE1  
GO:0051604 protein maturation   ATG15  
GO:0055086 nucleobase-containing small molecule metabolic process IMD2 IMD2, IMD3, NMA2, NPY1, PNC1, PRS2, PYC1, YNK1 IMD2, NMA1, NMA2, PGI1
GO:0070271 protein complex biogenesis   CYC3  
GO:0071554 cell wall organization or biogenesis   CWH41, PRS2 CHS5
Un-identified, down-regulated genes* BDH1 AAD15 AAD15 PHO11 AAD15 FEN1
Summary Down-regulated 8 36 29
Up-regulated 0 23 24
  1. Note: the genes marked as bold and italic have over 10 fold changes of expression, while the others have less than 10 fold changes of expression.
  2. *: some of the genes that were down-/up- regulated cannot be mapped into GO slim files.
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Biotechnology for Biofuels and Bioproducts

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