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Table 5 Gene Ontology (GO) Biological Processes enriched in clusters of differential co-expression protein interaction modules

From: Dynamic protein interaction modules in human hepatocellular carcinoma progression

Cluster GOID Term # expec-ted genes # genes Adjusted p-value *
I GO:0071842 cellular component organization at cellular level 23.3 44 0.0002
I GO:0007346 regulation of mitotic cell cycle 2.6 12 0.0004
I GO:2000241 regulation of reproductive process 1.2 8 0.0006
I GO:0009968 negative regulation of signal transduction 4.3 15 0.0006
I GO:0043066 negative regulation of apoptotic process 4.9 16 0.0006
I GO:0031577 spindle checkpoint 0.4 5 0.0007
I GO:0032088 negative regulation of NF-kappaB transcription factor activity 0.4 5 0.0007
I GO:0000086 G2/M transition of mitotic cell cycle 1.3 8 0.0007
I GO:0048522 positive regulation of cellular process 23.2 41 0.0007
I GO:0006366 transcription from RNA polymerase II promoter 10.2 24 0.0007
I GO:0042221 response to chemical stimulus 20.2 37 0.0008
I GO:0031623 receptor internalization 0.4 5 0.0008
I GO:0048468 cell development 10.5 24 0.0008
I GO:0050658 RNA transport 1.0 7 0.0008
I GO:0016032 viral reproduction 3.7 13 0.0009
II GO:0043065 positive regulation of apoptotic process 2.0 11 0.0003
II GO:0006366 transcription from RNA polymerase II promoter 4.3 15 0.0005
III GO:0016567 protein ubiquitination 4.5 17 0.0001
III GO:0000075 cell cycle checkpoint 2.7 13 0.0001
III GO:0042981 regulation of apoptotic process 12.9 30 0.0001
III GO:0000165 MAPK cascade 4.4 16 0.0001
III GO:0032268 regulation of cellular protein metabolic process 12.6 29 0.0001
III GO:0010627 regulation of intracellular protein kinase cascade 5.7 18 0.0002
III GO:0050863 regulation of T cell activation 2.4 11 0.0002
III GO:0007346 regulation of mitotic cell cycle 3.3 13 0.0002
III GO:0044419 interspecies interaction between organisms 4.4 15 0.0003
III GO:0006511 ubiquitin-dependent protein catabolic process 4.0 14 0.0003
III GO:0045892 negative regulation of transcription, DNA-dependent 7.7 20 0.0005
III GO:0007265 Ras protein signal transduction 2.8 11 0.0006
III GO:0007173 epidermal growth factor receptor signaling pathway 1.9 9 0.0007
III GO:0051090 regulation of sequence-specific DNA binding transcription factor activity 3.3 12 0.0007
III GO:0009967 positive regulation of signal transduction 6.7 18 0.0007
III GO:0016310 phosphorylation 13.6 28 0.0008
III GO:0045732 positive regulation of protein catabolic process 0.8 6 0.0008
III GO:0030518 intracellular steroid hormone receptor signaling pathway 1.1 7 0.0008
III GO:0042770 signal transduction in response to DNA damage 1.5 8 0.0009
III GO:0080134 regulation of response to stress 6.9 18 0.0009
III GO:0008285 negative regulation of cell proliferation 5.1 15 0.0009
IV* GO:0044419 * interspecies interaction between organisms 2.1 11 0.0020
IV* GO:0000904 * cell morphogenesis involved in differentiation 3.3 12 0.0099
IV* GO:0007165 * signal transduction 18.8 33 0.0099
V GO:0065008 regulation of biological quality 4.1 13 0.0008
V GO:0001775 cell activation 1.4 8 0.0009
V GO:0018193 peptidyl-amino acid modification 1.0 7 0.0009
V GO:0048011 nerve growth factor receptor signaling pathway 0.5 5 0.0009
V GO:0043066 negative regulation of apoptotic process 1.1 7 0.0009
V GO:0000165 MAPK cascade 0.8 6 0.0009
V GO:0042060 wound healing 1.2 7 0.0009
V GO:0045860 positive regulation of protein kinase activity 0.8 6 0.0009
V GO:0071375 cellular response to peptide hormone stimulus 0.5 5 0.0009
  1. * Threshold value for adjusted p-value is 0.01 (Cluster IV) or 0.001 (clusters I, II, III, and V). No GO term was found to be enriched for cluster VI with either threshold value.