Skip to main content

Table 3 Enrichment of the PPI subnets (Coum, SN.1 ~ SN9; Syr, SN.10 ~ SN.11; Fer, SN.12 ~ SN.13; Van, SN.14 ~ SN.16)

From: Gene coexpression network analysis reveals a novel metabolic mechanism of Clostridium acetobutylicum responding to phenolic inhibitors from lignocellulosic hydrolysates

Subnet Enrichment itema Function annotation FDR
SN.1 BP GO:0044267 Cellular protein metabolic process 8.85E − 38
MF GO:0003735 Structural constituent of ribosome 5.39E − 33
CC GO:0005840 Ribosome 4.22E − 33
KEGG cac03010 Ribosome 3.87E − 35
UniProt KW-0687 Ribonucleoprotein 1.82E − 35
SN.2 BP GO:0006261 DNA-dependent DNA replication 4.78E − 02
SN.3 KEGG cac02040 Flagellar assembly 1.15E − 23
UniProt KW-0282 Flagellum 5.41E − 17
SN.4 BP GO:0006281 DNA repair 6.64E − 06
MF GO:0140097 Catalytic activity, acting on DNA 3.03E − 02
CC GO:1990391 DNA repair complex 4.70E − 03
KEGG cac03440 Homologous recombination 1.70E − 03
UniProt KW-0234 DNA repair 2.15E − 07
SN.5 CC GO:0005737 Cytoplasm 2.03E − 02
KEGG cac01230 Biosynthesis of amino acids 2.70E − 03
SN.6 BP GO:0090304 Nucleic acid metabolic process 8.50E − 04
MF GO:0008144 Drug binding 8.97E − 05
CC GO:0005737 Cytoplasm 9.30E − 03
KEGG cac00970 Aminoacyl-tRNA biosynthesis 1.20E − 03
UniProt KW-0030 Aminoacyl-tRNA synthetase 1.20E − 03
SN.7 KEGG cac00523 Polyketide sugar unit biosynthesis 6.80E − 04
UniProt KW-0808 Transferase 5.10E − 03
SN.8 KEGG cac01130 Biosynthesis of antibiotics 3.56E − 06
UniProt KW-0501 Molybdenum cofactor biosynthesis 2.06E − 02
SN.9 UniProt KW-0418 Kinase 6.50E − 04
SN.10 BP GO:0034645 Cellular macromolecule biosynthetic process 9.66E − 13
MF GO:0003735 Structural constituent of ribosome 2.38E − 13
CC GO:0005840 Ribosome 2.08E − 13
KEGG cac03010 Ribosome 1.15E − 13
SN.11 KEGG cac00500 Starch and sucrose metabolism 5.14E − 06
UniProt KW-0732 Signal 8.54E − 09
SN.12 None   
SN.13 UniProt KW-0808 Transferase 4.20E − 02
SN.14 BP GO:0009260 Ribonucleotide biosynthetic process 3.64E − 06
MF GO:0016879 Ligase activity, forming carbon–nitrogen bonds 8.81E − 07
KEGG cac00230 Purine metabolism 8.75E − 13
UniProt KW-0658 Purine biosynthesis 1.76E − 17
SN.15 BP GO:0030435 Sporulation resulting in formation of a cellular spore 3.17E − 05
MF GO:0016987 Sigma factor activity 5.00E − 04
UniProt KW-0749 Sporulation 6.55E − 06
SN.16 BP GO:1901564 Organonitrogen compound metabolic process 2.30E − 03
MF GO:0016758 Transferase activity, transferring hexosyl groups 6.30E − 03
KEGG cac00400 Phenylalanine, tyrosine and tryptophan biosynthesis 5.52E − 05
UniProt KW-0133 Cell shape 2.51E − 06
  1. aThe genes in each subnet were enriched in GO, KEGG and UniProt databases, and the items with minimum FDR (< 0.05) was listed