. 2014 Oct 4;15(1):336. doi: 10.1186/1471-2105-15-336

Table 4.

Functional terms of GO biological processes and KEGG/REACTOME pathways enriched in 25 selected regulatory modules (FDR < 0.05)

Module	Term	Representative genes	p-value	FDR
Module103	GO:0008283 ~ cell proliferation	CREBBP	0.000353	0.00498
Module103	GO:0006357 ~ regulation of transcription from RNA polymerase II promoter	CREBBP, EP300	0.003488	0.04824
Module106	GO:0019221 ~ cytokine-mediated signaling pathway	IRAK4	0.001318	0.0192
Module106	hsa04630:Jak-STAT signaling pathway	IFNAR1, STAT2, IRF9	0.002251	0.0177
Module130	GO:0006915 ~ apoptosis	HSPE1	0.001585	0.01762
Module159	GO:0007249 ~ I-kappaB kinase/NF-kappaB cascade	IRF3, TRAF2, TICAM1, BCL3	3.58E-08	5.43E-07
	GO:0043068 ~ positive regulation of programmed cell death	TRAF2, TICAM1, BCL3	1.46E-07	2.21E-06
	GO:0002263 ~ cell activation during immune response	TICAM1, BCL3	2.23E-05	0.00034
	GO:0002366 ~ leukocyte activation during immune response	TICAM1, BCL3	2.23E-05	0.00034
	hsa04622:RIG-I-like receptor signaling pathway	IRF3, TRAF2, MAVS	2.27E-05	0.00021
	GO:0001819 ~ positive regulation of cytokine production	TRAF2, MAVS, TICAM1, BCL3	0.000347	0.00526
	GO:0051251 ~ positive regulation of lymphocyte activation	TRAF2, TICAM1	0.000433	0.00655
	GO:0045321 ~ leukocyte activation	TICAM1, BCL3	0.00047	0.00711
	GO:0006955 ~ immune response	MAVS, TICAM1, BCL3	0.000483	0.00731
	GO:0009615 ~ response to virus	IRF3, MAVS, TICAM1, BCL3	0.000609	0.0092
	REACT_6900:Signaling in Immune system	IRF3, TICAM1	0.001402	0.00804
Module171	hsa04310:Wnt signaling pathway	JUN, MAPK10, DVL2	0.000233	0.00246
	hsa04010:MAPK signaling pathway	JUN, MAPK10, MAPK1	0.001514	0.01594
	GO:0034097 ~ response to cytokine stimulus	JUN	0.00196	0.03023
	GO:0002237 ~ response to molecule of bacterial origin	JUN, MAPK1	0.002673	0.04102
Module173	GO:0006954 ~ inflammatory response	CEBPB, CCL5, F8, BDKRB1, ITGB2, HIF1A, TF, F3, C1RL, IL8	3.00E-05	0.00048
	GO:0009611 ~ response to wounding	CEBPB, CCL5, F8, BDKRB1, IGFBP1, ITGB2, NRG1, HIF1A, TF, F3, C1RL, IL8	5.28E-05	0.00085
	GO:0051240 ~ positive regulation of multicellular organismal process	CCL5, PTGS2, NRG1, HIF1A, MYLK2, TF, F3, IL27RA	0.000197	0.00316
	GO:0006952 ~ defense response	CEBPB, CCL5, F8, BDKRB1, ITGB2, HIF1A, TF, F3, IL27RA, C1RL, IL8	0.000835	0.01331
	GO:0032101 ~ regulation of response to external stimulus	CCL5, VEGFA, PTGS2, NT5E, F3, IL8	0.001131	0.01799
	REACT_604:Hemostasis	STX4, SLC7A7, F8, VEGFA, ITGB2, ALB, TF, F3	0.001131	0.00976
	GO:0002526 ~ acute inflammatory response	CEBPB, F8, TF, F3, C1RL	0.0014	0.02222
	GO:0043069 ~ negative regulation of programmed cell death	CEBPB, VEGFA, NRG1, ALB, KRT18, PPT1, PCSK6, F3	0.001937	0.03062
Module174	GO:0051726 ~ regulation of cell cycle	SMAD3, CDK4	1.10E-05	0.00016
	GO:0031328 ~ positive regulation of cellular biosynthetic process	SMAD3, CDK4	0.000612	0.00894
	GO:0006350 ~ transcription	SMAD3, ASH2L	0.000854	0.01245
Module175	GO:0000122 ~ negative regulation of transcription from RNA polymerase II promoter	CTNNB1,	0.002252	0.02972
Module178	GO:0051252 ~ regulation of RNA metabolic process	STAT1, UBE2I, HDAC3, PIAS2, DAXX, SP100	5.05E-05	0.00076
	REACT_11061:Signalling by NGF	HDAC3, AKT1	0.000413	0.00293
	GO:0007049 ~ cell cycle	DAXX, UBE2I, HDAC3, AKT1	0.0005	0.00753
	hsa04630:Jak-STAT signaling pathway	STAT1, AKT1, PIAS2	0.004991	0.04684
Module179	GO:0006974 ~ response to DNA damage stimulus	RAD54L, FANCI, XAB2, BCCIP, BRCA1, XRCC1, EEPD1, UPF1, RAD51, TOP2A, FANCD2, RAD54B	3.39E-08	4.91E-07
	REACT_216:DNA Repair	FANCI, XAB2, BRCA1, XRCC1, POLR2K, RAD51, POLR2A, FANCD2	1.64E-07	1.25E-06
	GO:0033554 ~ cellular response to stress	FANCI, RAD54L, XAB2, EEPD1, BRCA1, XRCC1, TOP2A, RAD54B, DHX9, BCCIP, UPF1, RAD51, FANCD2	2.71E-07	3.92E-06
	GO:0007049 ~ cell cycle	FANCI, RAD54L, KIF15, BRCA1, CHTF18, RCC1, RAD54B, CIT, BCCIP, UPF1, TUBB, RAD51, FANCD2	7.43E-06	0.00011
Module180	GO:0010604 ~ positive regulation of macromolecule metabolic process	NUP62	7.41E-05	0.0011
Module182	GO:0006303 ~ double-strand break repair via nonhomologous end joining	PRKDC	1.88E-06	2.83E-05
	GO:0045935 ~ positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	ILF2, RELA, NFKB1, PRKDC	0.000934	0.01395
	GO:0002562 ~ somatic diversification of immune receptors via germline recombination within a single locus	PRKDC	0.001732	0.02573
Module184	GO:0022402 ~ cell cycle process	MLH1, MAP2K6	0.001302	0.01777
Module185	GO:0007243 ~ protein kinase cascade	SRC, IKBKB, NFKBIA	0.001885	0.02759
Module186	REACT_1538:Cell Cycle Checkpoints	MCM4, MCM3, MCM5, MCM7, MCM2	9.90E-23	7.84E-22
Module186	GO:0006260 ~ DNA replication	MCM4, MCM3, MCM5, MCM7, MCM2	1.13E-21	1.51E-20
Module189	GO:0032268 ~ regulation of cellular protein metabolic process	CBS	0.00036	0.00532
Module190	GO:0008380 ~ RNA splicing	SFPQ	2.23E-06	3.19E-05
Module200	REACT_6185:HIV Infection	NUP188, NUP205	0.000592	0.00484
Module206	hsa04350:TGF-beta signaling pathway	SMURF2, SMAD6	0.001698	0.00872
Module241	GO:0006913 ~ nucleocytoplasmic transport	NXT1, RAN	0.001111	0.01645
Module244	REACT_12472:Regulatory RNA pathways	POLR2H, POLR2I, POLR2B, POLR2D, POLR2L	5.52E-10	3.65E-09
	REACT_6143:Pausing and recovery of Tat-mediated HIV-1 elongation	POLR2H, POLR2I, POLR2B, POLR2D, POLR2L	4.94E-09	3.27E-08
	REACT_6167:Influenza Infection	POLR2H, POLR2I, POLR2B, POLR2D, POLR2L	4.39E-06	2.91E-05
Module253	GO:0000398 ~ nuclear mRNA splicing, via spliceosome	HNRNPM	0.003042	0.04485
Module267	hsa04920:Adipocytokine signaling pathway	RXRB	8.48E-06	7.22E-05
Module280	GO:0006984 ~ ER-nuclear signaling pathway	PAK1, EIF2AK3	0.001649	0.02486
Module303	hsa04144:Endocytosis	VPS28	0.000182	0.00041

'Module’ refers to the module indices we gave. 'Term’ refers to the enriched GO terms (e.g. GO:0008283), KEGG pathways (e.g. hsa04630), and REACTOME pathways (e.g. REACT_6900). Certain genes in the modules are listed as 'Representative genes’. 'p-value’ and 'FDR’ shows the statistical significance of the results.