Table S2. A listing of gene modules and enriched pathways generated using DAVID. Q denotes false discovery rate for enrichment computed using the Benjamini-Hochberg method.

Module 1:

Hub genes
ANKRD28 PRKG1 NCKAP1 CD109 C7orf41
Pathway/GO term Q Fold enrichment
GO:0003924~GTPase activity 0.001445 2.406233
GO:0032553~ribonucleotide binding 0.001490 1.398468
GO:0032555~purine ribonucleotide binding 0.001490 1.398468
GO:0019001~guanyl nucleotide binding 0.004458 1.898710
GO:0032561~guanyl ribonucleotide binding 0.004458 1.898710

Module 2:

Hub genes
TSPO SPSB3 OXLD1 CYBA HMHA1
Pathway/GO term Q Fold enrichment
GO:0008408~3'-5' exonuclease activity 0.058365 7.188815
REACT_6185:HIV Infection 0.055435 2.452700

Module 3:

Hub genes
RBBP6 RAD50 SAP130 SMARCC2 ZBTB4
Pathway/GO term Q Fold enrichment
GO:0051276~chromosome organization 0.089253 2.331097
REACT_152:Cell Cycle, Mitotic 0.056223 2.153489

Module 4:

Hub genes
BPTF PRRC2C PHF3 NCOR1 SPEN
Pathway/GO term Q Fold enrichment
GO:0006350~transcription 0.000045 1.863874
GO:0016568~chromatin modification 0.001424 3.712200
GO:0030554~adenyl nucleotide binding 0.001751 1.761984
GO:0001882~nucleoside binding 0.002074 1.753447
GO:0001883~purine nucleoside binding 0.002265 1.735571

Module 5:

Hub genes
BRD8 KIAA0040 AHCYL1 UTP14C HMG20A
Pathway/GO term Q Fold enrichment
GO:0034470~ncRNA processing 0.040033 3.974849
GO:0034660~ncRNA metabolic process 0.050615 3.447173

Module 6:

Hub genes
PLXNC1 CLEC7A HCK NCF2 TNFAIP2
Pathway/GO term Q Fold enrichment
GO:0006955~immune response 0.000003 2.933714
GO:0006952~defense response 0.000008 2.970364
GO:0009611~response to wounding 0.000067 2.980967
GO:0002684~positive regulation of immune system process 0.000180 4.148930
GO:0045321~leukocyte activation 0.000186 4.080352

Module 7:

Hub genes
CREBBP CHD2 SPTAN1 KAT6A EP400
Pathway/GO term Q Fold enrichment
GO:0016568~chromatin modification 0.008159 3.922096
GO:0032555~purine ribonucleotide binding 0.011768 1.706878
GO:0032553~ribonucleotide binding 0.011768 1.706878
GO:0017076~purine nucleotide binding 0.012962 1.667249
GO:0005524~ATP binding 0.013516 1.818645

Module 8:

Hub genes
C14orf1 PTBP1 ZNF490 TRIM4 SSR1

No pathway/GO term enrichment

Module 9:

Hub genes
HNRNPM CERS5 GGA2 TADA2B LAS1L
Pathway/GO term Q Fold enrichment
GO:0006281~DNA repair 0.083289 3.810704

Module 10:

Hub genes
ZNF609 NASP EIF3A IK SAFB
Pathway/GO term Q Fold enrichment
GO:0008380~RNA splicing 0.000000 7.248622
GO:0016071~mRNA metabolic process 0.000000 5.828750
GO:0006396~RNA processing 0.000000 4.659513
GO:0006397~mRNA processing 0.000000 6.107725
GO:0003723~RNA binding 0.000013 3.561640

Module 11:

Hub genes
EXOC1 ST8SIA4 MARCH1 KCNJ2 ZFYVE16
Pathway/GO term Q Fold enrichment
P00015:Circadian clock system 0.020088 23.04032

Module 12:

Hub genes
THAP5 PTPRCAP ERO1L CHURC1 ZNF624
Pathway/GO term Q Fold enrichment
GO:0008270~zinc ion binding 0.000004 2.203951
GO:0006350~transcription 0.000107 2.226967
GO:0046914~transition metal ion binding 0.000117 1.900563
GO:0046872~metal ion binding 0.000261 1.616241
GO:0003677~DNA binding 0.000268 1.970821

Module 13:

Hub genes
SNHG8 CCDC109B RPS19BP1 EIF3E ZNF277
Pathway/GO term Q Fold enrichment
GO:0006412~translation 0.000003 6.130514
GO:0003723~RNA binding 0.026805 2.805854
GO:0003735~structural constituent of ribosome 0.034647 5.995844
REACT_71:Gene Expression 0.000227 3.832331
REACT_17015:Metabolism of proteins 0.005578 4.120786

Module 14:

Hub genes
CCDC25 SH3KBP1 RTF1 FLOT2 SUPT16H
Pathway/GO term Q Fold enrichment
GO:0000166~nucleotide binding 0.013045 1.945216

Module 15:

Hub genes
FAM196B ANGPT2 TTN TENM1 A2M

No pathway/GO term enrichment

Module 16:

Hub genes
RGS14 PPP1R12C PCED1A LIMD2 MTA1

No pathway/GO term enrichment

Module 17:

Hub genes
JMJD1C TCEB3 CCDC88A CD68 TSC1

No pathway/GO term enrichment

Module 18:

Hub genes
FKBP15 ZCCHC6 OSCAR SIRPB1 TRIM21

No pathway/GO term enrichment

Module 19:

Hub genes
ZHX2 PACS1 TTC3 CYFIP2 DOCK9
Pathway/GO term Q Fold enrichment
GO:0017159~pantetheine hydrolase activity 0.034662 145.8764

Module 20:

Hub genes
HNMT AIF1 CSTA TNFSF13B CPVL
Pathway/GO term Q Fold enrichment
GO:0006955~immune response 0.000980 3.734438

Module 21:

Hub genes
FLII HCLS1 PI4KB STK10 EHMT1
Pathway/GO term Q Fold enrichment
GO:0043039~tRNA aminoacylation 0.056320 15.159121
GO:0006418~tRNA aminoacylation for protein translation 0.056320 15.159121
GO:0043038~amino acid activation 0.056320 15.159121
GO:0009890~negative regulation of biosynthetic process 0.059687 3.407495
GO:0000278~mitotic cell cycle 0.065513 4.146225

Module 22:

Hub genes
DERL1 SEC23B DPY19L4 UNC50 MAGT1

No pathway/GO term enrichment

Module 23:

Hub genes
METTL9 BZW1 UQCRQ TMEM167B PSMA1
Pathway/GO term Q Fold enrichment
GO:0070003~threonine-type peptidase activity 0.001006 42.70724
GO:0004298~threonine-type endopeptidase activity 0.001006 42.70724
GO:0051351~positive regulation of ligase activity 0.012491 13.89863
GO:0051340~regulation of ligase activity 0.013689 12.52593
GO:0051438~regulation of ubiquitin-protein ligase activity 0.013720 13.00769

Module 24:

Hub genes
CNTRL KTN1 EEA1 TPR CAST
Pathway/GO term Q Fold enrichment
GO:0006396~RNA processing 0.000001 6.569241
GO:0008380~RNA splicing 0.000195 8.187060
GO:0016071~mRNA metabolic process 0.001393 6.284122
GO:0006397~mRNA processing 0.002343 6.584891
GO:0003723~RNA binding 0.016245 3.791423

Module 25:

Hub genes
SEPHS2 HIF1AN HNRNPA2B1 RAB27A APBB1IP
Pathway/GO term Q Fold enrichment
GO:0008380~RNA splicing 0.002414 6.468788
GO:0000377~RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 0.002449 9.824256
GO:0000398~nuclear mRNA splicing, via spliceosome 0.002449 9.824256
GO:0000375~RNA splicing, via transesterification reactions 0.002449 9.824256
GO:0006397~mRNA processing 0.004676 5.723164

Module 26:

Hub genes
GAA CORO1B SH3TC1 SLC16A3 HK3

No pathway/GO term enrichment

Module 27:

Hub genes
BMP2K FGD4 PLXDC2 CPEB4 ZNF117

No pathway/GO term enrichment

Module 28:

Hub genes
LRRN3 FAIM3 DYRK2 ATP8B2 GPR183

No pathway/GO term enrichment

Module 29:

Hub genes
PFDN1 HADHA URI1 BLMH ZCCHC7

No pathway/GO term enrichment

Module 30:

Hub genes
GLB1 ZDHHC7 PSEN1 ARSD TOR1B
Pathway/GO term Q Fold enrichment
REACT_11061:Signalling by NGF 0.024589 6.435606

Module 31:

Hub genes
SH2D1B AKR1C3 KLRD1 PRR5L MLC1

No pathway/GO term enrichment

Module 32:

Hub genes
ATP5A1 WDR61 IER3IP1 GHITM ATP5B

No pathway/GO term enrichment

Module 33:

Hub genes
BTN2A1 PRPF38B ZDHHC5 ELF4 IL17RA

No pathway/GO term enrichment

Module 34:

Hub genes
RBM3 CHMP1B VOPP1 ATXN10 SPG21

No pathway/GO term enrichment

Module 35:

Hub genes
UBR4 ANKRD36B TNRC6B ITPR2 HECTD4
Pathway/GO term Q Fold enrichment
GO:0044257~cellular protein catabolic process 0.000114 6.205286
GO:0030163~protein catabolic process 0.000119 6.015735
GO:0051603~proteolysis involved in cellular protein catabolic process 0.000162 6.236312
GO:0043632~modification-dependent macromolecule catabolic process 0.000202 6.518793
GO:0019941~modification-dependent protein catabolic process 0.000202 6.518793

Module 36:

Hub genes
FAM107B RALA SAP30L TMED10 UBE2D2

No pathway/GO term enrichment

Module 37:

Hub genes
PARP9 RSAD2 IFIT3 MX1 IFIT2
Pathway/GO term Q Fold enrichment
GO:0009615~response to virus 0.000000 30.394308
GO:0006955~immune response 0.000000 8.002366
GO:0006952~defense response 0.000023 6.284785
GO:0032555~purine ribonucleotide binding 0.000161 3.159540
GO:0032553~ribonucleotide binding 0.000161 3.159540

Module 38:

Hub genes
CEP78 NCAM1 S1PR5 ATP2B4 COLQ

No pathway/GO term enrichment

Module 39:

Hub genes
SCAF4 WASF2 HNRNPD TARDBP MDC1

No pathway/GO term enrichment

Module 40:

Hub genes
H6PD MTF1 BLOC1S3 ZDHHC5 IPO7

No pathway/GO term enrichment

Module 41:

Hub genes
ABLIM1 IDS SYNRG CDC25B CBX5
Pathway/GO term Q Fold enrichment
P00009:Axon guidance mediated by netrin 0.096641 24.4188

Module 42:

Hub genes
CMIP MITF ASAP1 MAML3 CYB5R3

No pathway/GO term enrichment

Module 43:

Hub genes
UCP2 CLSTN1 PDCL3 ARL4C HNRNPA0

No pathway/GO term enrichment

Module 44:

Hub genes
VTI1A STRN4 DHX8 RAPGEF2 REL

No pathway/GO term enrichment

Module 45:

Hub genes
C12orf49 PHF5A CRLS1 MRPL49 AGPAT6

No pathway/GO term enrichment

Module 46:

Hub genes
VMA21 HMGN4 TMEM8A NUDT21 TMEM248

No pathway/GO term enrichment

Module 47:

Hub genes
LRRC25 LPCAT2 MS4A7 SCARB2 TMTC1

No pathway/GO term enrichment

Module 48:

Hub genes
TBX21 GNLY KIR3DL1 USP28 CTSW
Pathway/GO term Q Fold enrichment
GO:0032393~MHC class I receptor activity 0.079595 69.427807
REACT_6900:Signaling in Immune system 0.018197 6.600622

Module 49:

Hub genes
RRAGA SCAMP2 COQ5 SS18L2 SERBP1

No pathway/GO term enrichment

Module 50:

Hub genes
PPP2R3C PSMA6 PPP2R4 PSMD8 MRPS22
Pathway/GO term Q Fold enrichment
GO:0046914~transition metal ion binding 0.002344 2.830354
GO:0008270~zinc ion binding 0.015487 2.808957
GO:0043167~ion binding 0.025197 1.967983
GO:0043169~cation binding 0.026106 1.997180
GO:0046872~metal ion binding 0.030802 2.015994

Module 51:

Hub genes
UNC50 TMEM30A RNFT1 MIR17HG STARD3NL

No pathway/GO term enrichment

Module 52:

Hub genes
BCL2A1 RNF149 PNPLA8 RELT ATG16L2
Pathway/GO term Q Fold enrichment
GO:0030163~protein catabolic process 0.094070 5.855553

Module 53:

Hub genes
LRRK2 DMXL2 WDFY3 AQP9 GLUL
Pathway/GO term Q Fold enrichment
GO:0001882~nucleoside binding 0.008226 3.377471
GO:0001883~purine nucleoside binding 0.011522 3.400677
GO:0030554~adenyl nucleotide binding 0.019795 3.452431
GO:0017076~purine nucleotide binding 0.031833 2.838626
GO:0032559~adenyl ribonucleotide binding 0.043092 3.077402

Module 54:

Hub genes
P4HB ACAA2 SUMF1 UQCRC1 PDIA3
Pathway/GO term Q Fold enrichment
GO:0051235~maintenance of location 0.058313 27.274194
GO:0045184~establishment of protein localization 0.062445 5.107261
GO:0008104~protein localization 0.063389 4.452930
GO:0045454~cell redox homeostasis 0.073617 27.707117

Module 55:

Hub genes
MS4A3 HDC CCR3 CLC CPA3
Pathway/GO term Q Fold enrichment
h_il5Pathway:IL 5 Signaling Pathway 0.025946 47.9

Module 56:

Hub genes
ABRACL TNFRSF14 PPP1R12C C6orf211 HNRNPF

No pathway/GO term enrichment

Module 57:

Hub genes
KIAA0430 XPO7 GSK3B IDS HIPK1

No pathway/GO term enrichment

Module 58:

Hub genes
ZBTB11 SENP7 ZNF92 ESCO1 RAB11FIP2
Pathway/GO term Q Fold enrichment
GO:0045449~regulation of transcription 0.059122 2.836951
GO:0030163~protein catabolic process 0.064677 5.931599
GO:0044257~cellular protein catabolic process 0.067594 6.118498
GO:0051603~proteolysis involved in cellular protein catabolic process 0.082019 6.149091
GO:0043632~modification-dependent macromolecule catabolic process 0.089506 6.427621

Module 59:

Hub genes
CEP63 MIA3 DNAJC7 RAB5C TBCA
Pathway/GO term Q Fold enrichment
GO:0034621~cellular macromolecular complex subunit organization 0.002152 11.532822
GO:0034622~cellular macromolecular complex assembly 0.002226 12.947225
GO:0065003~macromolecular complex assembly 0.005082 7.075776
GO:0043933~macromolecular complex subunit organization 0.005771 6.627312
GO:0034728~nucleosome organization 0.012409 25.297803

Module 60:

Hub genes
COMMD8 MRPS35 FAU STXBP3 MRPL13

No pathway/GO term enrichment

Module 61:

Hub genes
MDH1 RAN IARS2 OSTC DDOST

No pathway/GO term enrichment

Module 62:

Hub genes
FBXL5 PGK1 OAZ2 NDUFS1 LY86

No pathway/GO term enrichment

Module 63:

Hub genes
LTF OLFM4 CEACAM8 CRISP3 BPI
Pathway/GO term Q Fold enrichment
GO:0009617~response to bacterium 0.000000 35.046632
GO:0006952~defense response 0.000000 13.198049
GO:0042742~defense response to bacterium 0.000000 48.314286
GO:0006955~immune response 0.000205 8.822609
GO:0030246~carbohydrate binding 0.001842 14.670056