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Table 2 Gene ontology analysis of transcriptional responses of CTY and INVSc1 hosts to xylose metabolism

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

GO ID Description CW vs CC CW vs CI IW vs IC IW vs II
Up-regulated
GO:0000902 cell morphogenesis FKS1    
GO:0005975 carbohydrate metabolic process ERR1, FKS1, GPH1, GPM1, IMA1, MAL12, PYK2, SUC2, CIT1 ALG13, ALG2, CIT1, CWH41, GPH1, KRE6, PYC1, STT3   
GO:0006091 generation of precursor metabolites and energy ATF1, ERR1, FRE3, GPH1, GPM1, PYK2, CIT1 CIT1, GPH1, OLE1   
GO:0006457 protein folding   CPR7   
GO:0006486 protein glycosylation   ALG2, CWH41, STT3   
GO:0006520 cellular amino acid metabolic process GDH1, CIT1 ASN1, CIT1, GDH3, LEU1, MET13, MET16, TRP5, YGR012W   
GO:0006629 lipid metabolic process MCR1, YPC1 ALG13, ALG2, ECT1, ERG26, ERG4, MET13, MET16, OLE1, POX1   
GO:0006811 ion transport FRE3    
GO:0006873 cellular ion homeostasis FRE3    
GO:0006897 endocytosis FKS1    
GO:0006979 response to oxidative stress AHP1, MCR1    
GO:0008033 tRNA processing   PUS2   
GO:0008380 RNA splicing MNE1    
GO:0009311 oligosaccharide metabolic process IMA1, MAL12, SUC2 ALG2, CWH41   
GO:0009451 RNA modification   PUS2   
GO:0018193 peptidyl-amino acid modification   CPR7   
GO:0023052 signaling PDE2    
GO:0042221 response to chemical stimulus AHP1, MCR1 MNL1   
GO:0045333 cellular respiration CIT1 CIT1   
GO:0051049 regulation of transport FKS1    
GO:0051603 proteolysis involved in cellular protein catabolic process   ATE1, MNL1   
GO:0051604 protein maturation   KEX1   
GO:0051186 cofactor metabolic process ACH1, ALD4, FDH1, CIT1 CIT1, HEM2, MET13, NMA2, NPY1, PNC1, PYC1   
GO:0055086 nucleobase-containing small molecule metabolic process ALD4, FDH1 NMA2, NPY1, PNC1, PYC1   
GO:0071554 cell wall organization or biogenesis   CWH41, KRE6   
Un-identified, up-regulated genes* POT1, SDH1 BAT1   
Down-regulated
GO:0005975 carbohydrate metabolic process CIT3    RPE1
GO:0006091 generation of precursor metabolites and energy CIT3    
GO:0006470 protein dephosphorylation    YMR1  
GO:0006520 cellular amino acid metabolic process   GSH2 CPA2, URA8 URA2
GO:0006605 protein targeting ACC1    
GO:0006629 lipid metabolic process ACC1, ARE2, CIT3, LRO1   URA8, YJR107W, YMR1 LCB3
GO:0006873 cellular ion homeostasis    SOD1  
GO:0006979 response to oxidative stress    SOD1  
GO:0006997 nucleus organization ACC1    
GO:0023052 signaling     LCB3
GO:0042221 response to chemical stimulus    SOD1  
GO:0045333 cellular respiration CIT3    
GO:0051169 nuclear transport ACC1    
GO:0051186 cofactor metabolic process ACC1, CIT3    RPE1
GO:0055086 nucleobase-containing small molecule metabolic process ACC1, URK1   ADO1, URA8 RPE1, URA2
GO:0071554 cell wall organization or biogenesis    SOD1  
Un-identified, down-regulated genes* NIT2
Summary Up-regulated 22 30 0 0
Down-regulated 5 1 6 4
  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.