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Table 1 Results of functional enrichment analysis for three clusters.

From: Computational gene network analysis reveals TNF-induced angiogenesis

Category Term #genes p-value
Cluster A    
GOTERM_BP_FAT GO:0008283: cell proliferation 13 0.0027
GOTERM_BP_FAT GO:0001775: cell activation 10 0.0039
GOTERM_BP_FAT GO:0006916: anti-apoptosis 8 0.0070
GOTERM_BP_FAT GO:0040007: growth 7 0.0144
KEGG_PATHWAY hsa05222: Small cell lung cancer 5 0.0442
GOTERM_BP_FAT GO:0001568: blood vessel development 7 0.0497
Cluster B    
GOTERM_BP_FAT GO:0007596: blood coagulation 5 0.00034
GOTERM_BP_FAT GO:0043066: negative regulation of apoptosis 8 0.0056
GOTERM_BP_FAT GO:0043069: negative regulation of programmed cell death 8 0.0060
GOTERM_BP_FAT GO:0060548: negative regulation of cell death 8 0.0061
GOTERM_BP_FAT GO:0045765: regulation of angiogenesis 4 0.0066
GOTERM_BP_FAT GO:0006916: anti-apoptosis 6 0.0083
GOTERM_BP_FAT GO:0008283: cell proliferation 8 0.0164
KEGG_PATHWAY hsa05200: Pathways in cancer 8 0.0237
GOTERM_BP_FAT GO:0016477: cell migration 6 0.0260
PIR_SUPERFAMILY PIRSF001719: fos transforming protein 2 0.0334
GOTERM_BP_FAT GO:0008284: positive regulation of cell proliferation 7 0.0396
INTERPRO IPR000837: Fos transforming protein 2 0.0443
Cluster C    
GOTERM_BP_FAT GO:0006916: anti-apoptosis 9 0.0001
GOTERM_BP_FAT GO:0043066: negative regulation of apoptosis 11 0.0001
GOTERM_BP_FAT GO:0043069: negative regulation of programmed cell death 11 0.0001
GOTERM_BP_FAT GO:0060548: negative regulation of cell death 11 0.0001
INTERPRO IPR011539: Rel homology 3 0.0014
INTERPRO IPR000451: NF-kappa-B/Rel/dorsal 3 0.0014
GOTERM_BP_FAT GO:0043123: positive regulation of I-kappaB kinase/NF-kappaB cascade 5 0.0035
GOTERM_BP_FAT GO:0043122: regulation of I-kappaB kinase/NF-kappaB cascade 5 0.0050
BIOCARTA h_nthiPathway: NFκB activation by Nontypeable Hemophilus influenzae 4 0.0066
GOTERM_BP_FAT GO:0016477: cell migration 7 0.0087
GOTERM_BP_FAT GO:0030155: regulation of cell adhesion 5 0.0117
KEGG_PATHWAY hsa05222: Small cell lung cancer 5 0.0125
PIR_SUPERFAMILY PIRSF037644: inhibitor of apoptosis protein with CARD domain 2 0.0129
GOTERM_CC_FAT GO:0033256: I-kappaB/NF-kappaB complex 2 0.0233
KEGG_PATHWAY hsa05200: Pathways in cancer 9 0.0234
GOTERM_BP_FAT GO:0030334: regulation of cell migration 5 0.0235
  1. Functional enrichment for each cluster was evaluated by using DAVID. The following three clusters have enrichment of cell proliferation, apoptosis and angiogenesis that are important function for interpreting the estimated TNF-induced gene networks.