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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