Table II.
Gene networks overrepresented by differentially expressed genes
| # | Genes in Network* | Score | Focus genes | Functions |
|---|---|---|---|---|
| 1 | 26s Proteasome, BCR, BIRC2, CASP5, CASP6, Caspase, CD79B, COX5B, DNAJC3, DYNC1I2, DYNLL1, FKBP5, GLA, Hsp70, Hsp90, HSPA8, Igm, Ikb, IL18RAP, LRRK2, LTA4H, NFkB (complex), NFKBIA, NFKBIZ, NGLY1, PCYT1A, peptidase, PI3, RNF38, ST13, TNFRSF10C, TPP1, TXNRD1, UBE2D3 (includes EG:7323), Ubiquitin | 44 | 25 | Cellular Function and Maintenance, Hematological System Development and Function, Hematopoiesis |
| 2 | ACTR2, ACTR3, AIM1 (includes EG:202), Arp2/3, ARPC2, CASC3, CSDE1, CTSH, Cyclin A, Cyclin E, E2f, E2F3, EAPP, EGLN2, ELF4, Estrogen Receptor, EXOSC8, F Actin, GK, HIRA, HISTONE, Histone h3, Histone h4, IFI16, MBD1, MEF2C, NCOA1, P38 MAPK, PLEKHO1, Rb, RNA polymerase II, SMARCA4, TAF5L, TMEM126A, Vegf | 35 | 22 | Cellular Development, Skeletal and Muscular System Development and Function, Cell-To-Cell Signaling and Interaction |
| 3 | AHSA1, ATP5I, Calcineurin protein(s), Calpain, Cbp/p300, CD3, CD52, CEBPB, CLNS1A, CREB1, EIF4A2, Eif4g, ENTPD1, ERK1/2, GC-GCR dimer, HNRNPA3, LAT2, MKNK1, Nfat (family), NFATC3, NMI, PDGFA, Pias, PRKCH, RAB1A, RPS6, Rsk, RUNX3, SLC2A3, SNRPG, STAT5a/b, TCF7, TCR, TDG, VitaminD3-VDR-RXR | 32 | 22 | Digestive System Development and Function, Gene Expression, Energy Production |
| 4 | AQP3, ATP9A, CXORF26, DHRS3, EBNA1BP2, FNG, FSH, GDE1, GFI1B, GK7P, GRB2, GTPBP4, H1F0, hCG, Lh, LOC81691, LYAR, NOTCH1, PAPSS1 (includes EG:9061), PFKFB3, Pka, PP1 protein complex group, PPP1R16A, QRFP, RASSF2, RB1, RBM33, RFNG, SRP9, SRP14, SULF2, SUV420H1, TP53I11, VEGFA, ZNF143 | 23 | 16 | Cellular Development, Cellular Growth and Proliferation, Cancer |
| 5 | Alp, Ap1, ASCC2, ATL3, BCL6, BMP2K (includes EG:55589), Calmodulin, CYP1B1, ERK, GTPBP8, IFN Beta, IgG, IL1, IL12 (complex), IL1RN, IL4R, Immunoglobulin, Insulin, Interferon alpha, Jnk, KHDRBS1, KLHL2, LDL, Mapk, MDFIC, MIR124, Mmp, MMP25, Pdgf, PDGF BB, PI3K, Pkc(s), PTBP1, SEMA4D, VAMP3 | 22 | 15 | Cellular Development, Genetic Disorder, Inflammatory Disease |
| 6 | BZW2, C19ORF60, CEP63, COX11, COX15, COX10 (includes EG:1352), COX4I2, COX6A2, COX6B1, COX6B2, COX7A1, COX7A2, COX7A2L, COX7B, COX7B2 (includes EG:170712), COX8A, COX8B, COX8C, CTNNB1, Cytochrome c oxidase, FOXP1, HTT, ILF3, MAST3, MBTPS1, MDFI (includes EG:4188), MGAT5, MUT, NDUFB10, NPTN, PTCHD2, RASGRP2, TOMM7, TOMM20, WAC | 21 | 15 | Genetic Disorder, Neurological Disease, Skeletal and Muscular Disorders |
| 7 | ANP32B, CCDC88B, CD48, CD53, CDH1, CHTF18, CMKLR1, DDX11, DDX18, EEF1G, FAM160B1, GABARAPL2 (includes EG:11345), GBAS, HIVEP2, HNRNPAB, HPRT1, IL15, L-triiodothyronine, MGST3, MRPS22, MYC, NIPSNAP1, NOSIP, PDCD5, PFKP, Rfc, RFC2, RFX1, RFX2, RPL22, SCD2, SRM, TP53I3, TRIP12, TSPAN7 | 20 | 14 | DNA Replication, Recombination, and Repair, Gene Expression, Cell Death |
| 8 | AHCYL1, AIP, BTF3, CD93, Ck2, CLCN7, CYC1, CYTB, Cytochrome bc1, FRG1, FXR1, GPR56, HCG 25371, HMGN2, HOXA9, MEGF11, NUTF2, PTPRCAP, RPL37, RPL37A (includes EG:6168), SSB, SUGT1, TAL1, ubiquinol-cytochrome-c reductase, UQCR10, UQCR11, UQCRB, UQCRC1, UQCRC2, UQCRFS1, UQCRFSL1, UQCRH, UQCRQ, VHL | 18 | 13 | Cellular Function and Maintenance, Genetic Disorder, Metabolic Disease |
| 9 | ABHD6, APEH, BCCIP, C11ORF58, C9ORF78, CDK2, DPM1, DPM2, EIF5, GPX2, GPX7, GSTZ1 (includes EG:2954), HNF4A, KAP, KIAA0174, KIAA1012, LAPTM4A, LCMT2, MGST2, MGST3, MIPEP, MPP1, MRPL22, NAA25, NLN, PNO1, REXO2, RNGTT, SAP30BP, SLC35A1, SPCS3, SUPT5H, UBA5, USMG5, VPS29 | 18 | 13 | Genetic Disorder, Hepatic System Disease, Liver Cholestasis |
| 10 | ACSM3, ADAMDEC1, ADAMTS3, ANXA8, ART3, B3GNT1, beta-estradiol, C11ORF10, CNDP2, EGFBP2, FAM105B, FLOT2, GRAMD1C, HSF2BP, ITM2A, KDELR3, KRAS, LEPROT, METTL7A, MIR192 (includes EG:387187), MIR292 (includes EG:100049711), MME, MRVI1, MSGN1, MTMR4, MTRR, NPL, PNRC2 (includes EG:55629), progesterone, SOLH, SRI, TGFB1, TMEM164, WFDC2, ZEB2 | 18 | 13 | Cancer, Cardiovascular System Development and Function, Cell Morphology |
| 11 | ACAA1, ACSBG1, ACSL4, ATP6V1B2, C14ORF166, C6ORF48, CAPRIN1, CEP170, CFTR, CLTA, EMG1, ESYT1, GLG1, IDH2, MAN2B1, palmitic acid, PLA2G4C, PLOD1, PNPLA3, PSMB7, RPLP2, RPLP0 (includes EG:11837), RPS8, RPS18, SFXN3, SLC25A38, SLC27A2, SLC27A4, SLC2A4, TLN2, TMED2, TMED9, TMEM43, TMLHE, YWHAZ | 16 | 12 | Lipid Metabolism, Small Molecule Biochemistry, Carbohydrate Metabolism |
| 12 | AIFM3, amino acids, AMY1A, AMY2A, AMY2B (includes EG:280), ascorbic acid, B3GNT2, BHMT, CASP3, CASP8AP2, CDK11A, CUL1, DAPK2 (includes EG:23604), DNASE1L3, DPP7, DUSP22, EBAG9, EIF2AK1, EMILIN2, FBXL3, GMFG, IP6K3, MIRN101B, NR3C1, OOEP, PRKAR1B, RAB11A, RABGGTB, SEC62, SPPL2B, SRP72, SSH2, STK17B, TAOK1, WDR26 | 16 | 12 | Amino Acid Metabolism, Post-Translational Modification, Small Molecule Biochemistry |
| 13 | ABCB8, C14ORF106, CABC1, COX7A2, CTSW, DOK3, FAM86C, FKBP1B, HMGB2, HNF4A, IL2, INS1, LOC340571, MICAL1, NDUFB1, NDUFB5, POLE3, PPARGC1A, PPIL1, SAT1, SAT2, SDCCAG3 (includes EG:10807), SFRS4, SH3BGRL2, TACO1, TCF25, TMEM66, TP53, TP53INP1, TP53RK (includes EG:112858), TPRKB, VAMP5, VIM, WBP2, ZNF175 | 15 | 12 | Carbohydrate Metabolism, Hepatic System Development and Function, Organismal Functions |
| 14 | 5430435G22RIK, BTN3A3, CHST2, CIITA, CST7, CXCL10, DPP8, ERBB2, FNBP1, GBP6, GBP1 (includes EG:14468), GBP4 (includes EG:17472), IFI203, IFIT5, IFNB1, IRF6, MAP3K14, NNMT, OAS3 (includes EG:4940), PUM1, RHOV, RNF149, RNU1-1, RPL10L, RPL27A, RPL36AL, RPS15A (includes EG:6210), SEMA4C, SERPINB1, ST3GAL6, TNF, WFS1, ZNF330, ZXDA, ZXDC | 14 | 11 | Inflammatory Disease, Inflammatory Response, Connective Tissue Disorders |
| 15 | ANKRD13A, ARL4D, C20ORF30, CDS2, DUB, EML4, EP300, LAPTM5, NFYB, RBM14, SNX6, USP6, USP17, USP26, USP29, USP30, USP32, USP34, USP35, USP36, USP38, USP40, USP41, USP42, USP43, USP44, USP45, USP47, USP50, USP13 (includes EG:8975), USP27X, USP37 (includes EG:57695), USP51 (includes EG:158880), YIPF4, ZFP36 | 14 | 11 | Genetic Disorder, Reproductive System Disease, Amino Acid Metabolism |
*
The networks were generated using Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com). Each gene identifier was mapped to its corresponding gene object in the Ingenuity Pathways Knowledge Base (IPKB). These genes were overlaid onto a global molecular network developed from information contained in the IPKB. Network enrichment is then assessed using a network score (negative log of p-values of Fisher tests). Focus genes (in bold) are genes identified in our list of differentially expressed genes. Networks shown here are those with network scores > 3.0.