Electronic Supplemental Materials Table S5: Integrated Genomic Networks

Network
Id / Genes / Score / Focus genes / Top functions
1 / ACTN1,ASGR2,CCNA2,CCNB1,CDC2,CDC25A,CDC25B,CHEK1,CKS1B,CLDN4,CYC1,E2F4,EEF1A1,ELAVL1,FEN1,HNRPK,HTRA1,IGFBP6,ITPA,LOXL1,LTC4S,MXI1,PPIA,PPIG,PRODH,RAD51,RAD51AP1,RAD54L,RBM3,SERPINH1,SFRS3,TGFB1,TNFAIP2 (includes EG:7127),TXNIP,UBE2C / 54 / 35 / Cell Cycle,Cancer,Reproductive System Disease
2 / ANLN,AURKA,AURKAIP1,AURKB,BIRC5,BUB1,BUB1B,CCNB2,CCNG1,CDC20,CDCA8,CDK4,CENPA,CHD3,CTSF,DLG7,DNMT1,FUBP1,GNL3,GTSE1,HSP90AA1,HSPA9B (includes EG:3313),INCENP,KIF14,KIF23,MAD2L1,NASP,NUSAP1,PRC1,REV3L,THBS2,TK1,TP53,TUBB4,VRK1 / 54 / 35 / Cell Cycle,Cellular Movement,Cancer
3 / ANKRD1,C1QA,CDC45L,CENPF,CTGF,CTSD,DUSP1,FST,G1P2,HELLS,HGF,HSPB2,IGF2,IGFBP3,IGFBP4,INHBA,KIF22,MCM2,MCM3,MCM4,MCM5,MCM6,MMP1,MMP7,MMP13,ORC1L,PFDN6,PGAM1,PLAT,PLAUR,PSAP,RRM2,TFPI2,TIMP3,UHRF1 / 54 / 35 / Cancer,Cellular Movement,Cell Death
4 / ANXA2,ARG1,BCAT1,CCNA2,CDC2L1,CEBPA,CKS2,CREG1,CTSB,DDX21,E2F4,ESPL1,FBL,GADD45A,HNRPH1,HNRPK,LGMN,MTHFD1,MYC,NCL,NFYA,NFYC,NOL5A,PABPC4,PCBP2,PLAT,PTTG1,RPL14,RPS12,RPS4X,SERPINI1,SNRP70,TNC,TUBB2A,UBE2C / 25 / 22 / Gene Expression,Cell Cycle,Cardiovascular Disease
5 / ANXA3,ARID4A,BDP1,BRF1,BRMS1,CBFA2T3,CBX1,CBX5,CCNA1,CDC25A,CDC25C,CDK4,CDKN2D,CHAF1A,CHEK1,DNMT1,GJA1,GJA7,GTF3C2,HDAC8,HIST1H1B,HIST2H3C,HRAS,PHF5A,PLOD1,RAD51,RB1,RBBP4,RUNX1T1,SAP30,SDCCAG10,SHFM1,SUV39H1,TLK1,TOP2A / 18 / 18 / Cancer,Cell Cycle,Reproductive System Disease
6 / ACHE,AGER,APLP1,APP,CALB1,CLSTN1,CST3,CTSB,CTSL,DEFB103A,ELAVL1,EZH2,FPRL1,HIP2,IFIT1,IFNG,IL6,IRAK1,KIF11,LBP,LGALS1,LY96,MARCKS,MX1,NONO,PRTN3,PSME2,RXRA,SERPINA3G,SFPQ,SLPI,SPON1,TK1,TRPC4,TRPC5 / 16 / 17 / Immune Response,Neurological Disease,Organismal Injury and Abnormalities
7 / ANXA13,ARMET,CDKN1A,CHEK1,DNAJA3,ELAVL1,ELF3,GATA6,GEM,HCAP-D3,HCAP-H2,HDGF,HGFAC,HIF1A,IL1B,ING4,KIF2C,LOX,LUZP5,MAZ,MIA,NKIRAS1,P4HA1,PDE5A,PGF,PPP1R14B,RELA,ROCK2,SCYE1,SLPI,SMC2L1,SMC4L1,SPAG5,SPDEF,TNFAIP2 (includes EG:7127) / 15 / 16 / Cell Cycle,Cellular Assembly and Organization,DNA Replication, Recombination, and Repair
8 / AIF1,APEX1,BRD4,CHTF18,DCC1,DERPC,E2F1,FEN1,FGF2,HUS1,KIAA0101,MSH2,MSH3,MSH6,MUTYH,NES,PCNA,POLA2,POLM,RAD1,RANBP1,RECC5,RECQL,RFC2,RFC3,RFC4,RFC5,SCD,SLC19A1,TCP1,UNG,UNG2,UQCRQ,VHL,XRCC5 / 15 / 16 / DNA Replication, Recombination, and Repair,Cancer,Hematological Disease
9 / ADM,ANXA2,CALCR,CALCRL,DKC1,EXOSC5,FBL,GLE1L,HNRPD,IAPP,LOC499709,LSM1,LSM2,LSM3,LSM5,LSM6,LSM7,LSM8,MLF1,NCL,NOLC1,NUP155,NUPL2,PA2G4,PCBP1,PCBP2,RAMP1,RAMP2,SAFB2,SART3,SFRS12,SMN1,SNRPD2,SNRPE,TCOF1 / 15 / 16 / Cancer,Cell-To-Cell Signaling and Interaction,Skeletal and Muscular Disorders
10 / ABCE1,ADAM17,ADFP,AGER,ANXA5,CCL7,CDKN2C,FABP5,HDAC9,HMGB1,HMGB2,HNRPA1,HSPD1,KIF20A,KLF4,MMP7,MMP17,MYEF2,NUP98,NUP107,NUP133,NUP160,P4HA1,P4HA2,P4HA3,P4HB,PLA2G4A,PLAT,POLR2A,RANBP5,SCO2,SNCA,THBD,TIMP2,TNF / 14 / 15 / Amino Acid Metabolism,Post-Translational Modification,Small Molecule Biochemistry
11 / CA2,DHRS4,DPP4,EBP,EPHB2,HNRPF,HSPD1,HSPE1,IL15,IL12B,IRS1,MAPK1,MST1,NAGA,NTF5,PES1,PFN1,PSAP,PSMA1,PSMA4,PSMA5,PSMA6,PSMB1,PSMB2,PSMB3,PSMB4,PSMB5,PSMB6,PSMB7,PSMB8,PSMB9,PSMB10,PSME1,PSME2,UBTF / 14 / 15 / Cell-To-Cell Signaling and Interaction,Immune Response,Immune and Lymphatic System Development and Function
12 / ABCF2,ADA,BIRC3,CCNA2,CDC6,DHX36,DNMT1,DPP4,FAIM,FOXO1A,HNRPAB,HOXA5,HOXA9,IER2,IGF1,IL1A,INPPL1,KLF10,MEIS2,MPHOSPH1,NDN,PARP1,PBX1,PCNA,PDX1,PHLDA1,PPARGC1A,PRRX1,RBL2,RBM13,RPS3A,S100A8,SIRT1,TNNT1,USP1 / 14 / 15 / Cancer,Cell Death,Gene Expression
13 / AARS,APC,CDC25B,CKAP4,CLU,COL4A1,CTPS,DHRS9,DULLARD,EEF2,EEF1A1,EIF1,EIF1AX,EIF3S8,EIF3S10,EIF4A1,EIF4G1,EIF4G2,ESM1,F2,MKNK1,MYCN,NCL,RDH5,RPLP2,RPS7,RPS8,RUVBL2,SELE,SERPING1,SLC35A2,SPR,ST13,TM6SF1,YWHAZ / 14 / 15 / Protein Synthesis,Cell-To-Cell Signaling and Interaction,Gene Expression
14 / ACLY,ADM,CALB1,CASP3,CPSF1,CYP3A,DIDO1,ELL,FDFT1,FGF4,FOS,GNPAT,HGS,HMGCS1,INS1,LMNB1,MT1A,NDFIP2,NEDD4,NEDD4L,NEK6,NMI,NR0B2,NSDHL,PDHB,PKLR,RPS6,SCD,SFRP1,SGK,SLC2A2,SNCG,SREBF1,SREBF2,WEE1 / 12 / 14 / Gene Expression,Lipid Metabolism,Small Molecule Biochemistry
15 / ADSS,AUP1,BMP4,CCND2,CCNE1,CDCA1,COMP,CYB5B,E2F4,ENTPD2,FGF7,GADD45A,GH1,HMGA2,HOXA1,ID2,ID3,ITGA1,ITGA2,KNTC2,MAD1L1,MAD2L1,MATN1,MATN3,MLH1,MYB,NEK2,PCNA,PMF1,SHC1,SPBC24,SPBC25,TTK,XDH,ZWINT (includes EG:11130) / 12 / 14 / Cell Cycle,Cell Death,Cellular Assembly and Organization
16 / CD247,CLNS1A,CYCS,DBN1,DHX9,GEMIN4,GEMIN5,GSN,GSTO1,HNRPH3,HSP90AA1,KIAA1274,KRAS,LGALS1,MTHFD2,NXN,POP1,POP4,POP7,PRMT5,RPP14,RPP21,RPP30,RPP38,RPP40,SERPINB5,SMNDC1,SNRPB,SNRPD1,SNRPD2,SNRPD3,TDPX2,TPM2,VDAC1,WDR77 / 11 / 13 / Cell Death,Lipid Metabolism,Molecular Transport
17 / AKT1,CIAA1,CIAA2,COL10A1,COL11A2,COL1A1,COL1A2,COL2A1,COL3A1,COL5A3,CRYZ,ECT2,ESR2,FMR1,FOXG1B,FOXM1,GGT1,HINT1 (includes EG:3094),IGFBP7,IMPDH2,LRG1,NME6,P4HA1,P4HB,PELP1,PPARGC1A,RACGAP1,REXO4,RFX1,SMAD3,TGM2,TNFSF11,UCHL5,YBX1,ZBTB7B / 10 / 12 / Dermatological Diseases and Conditions,Skeletal and Muscular Disorders,Amino Acid Metabolism
18 / ARNT2,CASC3,FOS,GCG,IGFBP4,IPO13,MAGOH,NDUFA1,NFATC2,NXF1,RBM8A,SDS,SELENBP1,SIM1 / 6 / 6 / Amino Acid Metabolism,Small Molecule Biochemistry,Gene Expression
19 / TIMM10,TIMM13,TIMM23,TIMM8A / 2 / 2 / Auditory and Vestibular System Development and Function,Protein Trafficking,Cellular Compromise
20 / KATNA1,KATNB1 / 1 / 1 / Cellular Assembly and Organization,Cellular Function and Maintenance,Cellular Compromise
21 / BANF1,HIST1H1D / 1 / 1 / Viral Infection,Cell Cycle,Cellular Assembly and Organization
22 / FMNL3,PRPF40A / 1 / 1
23 / MRPS12,SPINK7 / 1 / 1 / Cancer,Cellular Growth and Proliferation,Tumor Morphology
24 / ARSA,SUMF1 / 1 / 1 / Genetic Disorder,Lipid Metabolism,Metabolic Disease
25 / ODF1,ODF2,SPAG4 / 1 / 1 / Cellular Development,Reproductive System Development and Function,Cellular Assembly and Organization
26 / PPIH,PRPF3,PRPF4,PRPF18,PRPF4B / 1 / 1 / RNA Post-Transcriptional Modification,Protein Trafficking,Post-Translational Modification