Table 4 Functional terms of GO biological processes and KEGG/REACTOME pathways enriched in 25 selected regulatory modules (FDR < 0.05)

Module103

GO:0008283 ~ cell proliferation

CREBBP

0.000353

0.00498

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

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

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