Table 1.
Top 6 networks identified by IPAa
| Molecules in network | Score | No. of focus molecules | Major functions |
|---|---|---|---|
| 26S proteasome, ABCC1, alpha catenin, alpha tubulin, ATPase, beta tubulin, CCT3, DERL1, ELF2, GATA2, GBAS, Gi-coupled receptor, Hdac, HHEX, HLA-DR, Hsp27, Hsp70, Hsp90, IL-8, KLK3, MAPK, MHC class I (family), NCKAP1, NDRG4, PARK2, Rsk, scavenger receptor class A, SIRPA, SSBP3, THBS2, TNF, TNFAIP3, UBE2D3, ubiquitin, VCP | 28 | 18 | Cellular movement, cardiovascular system development and function, organismal development |
| Adaptor protein 1, AMPK, ANP32A, ANXA2, APAF1, BIRC3, caspase, Cdk, cyclin A, cyclin D, cyclin E, cytochrome c, DNMT1, FASLG, FOXE1, FZR1, HBXIP, JNK, MCMBP, MIF, MTORC1, MUTYH, NADPH oxidase, OGG1, PARP14, PARP, PGD, PMAIP1, PRKAA, Rb, RMI1 (includes EG:306734), RPA, TH2 cytokine, TSH, XPC | 27 | 18 | Cancer, respiratory disease, organismal injury and abnormalities |
| 2′ 5′ oas, AIRE, CCL5, CLTCL1, CYP, EFCAB6, EIF2AK1, ferritin, HDL, hemoglobin, HSD17B2, IFN beta, IFNB1 (includes EG:15977), IL-6, IL-12 (family), immunoglobulin, ING4, alpha interferon, IRF3 dimer, JAK, LDL, MHC class I (complex), N-cor, Nr1h, Rxr, SEMA4A, SLC40A1, STAB1, STAT5a/b, STRA6, STX2, TBL1XR1, TPST1, USP18, vitamin D3-VDR-RXR | 26 | 17 | Cell-to-cell signaling and interaction, cellular movement, hematological system development and function |
| C1q, C1R, complement component 1, DDX58, DEFA1 (includes others), HIVEP2, IFI44, IFIH1, IFIT1, IFIT2, IFIT3, IFN alpha/beta, IFN type 1, IKK (family), IL-1R, IL-1/IL-6/TNF, IFN-α induced, IRAK, IRF, IRF1 (includes EG:16362), ISGF3, ITPKB, lymphotoxin, lymphotoxin-alpha1-beta2, MX1, NFκB (complex), NFκB-RelA, PTX3, RNF25, RSAD2, SENP1, TNF receptor, TRAF, UBE2, VSNL1 | 25 | 17 | Antimicrobial response, inflammatory response, infectious disease |
| ASRGL1, CCDC86, DAZ1/DAZ4, DAZAP1, DAZL, DDX50, DLG5, DLST, FADS3, FAM129A, FN3KRP, MPP2, MTR, MTRR, NDNL2, NSMCE1, NSMCE2, NSMCE4A, POLR1E, POP4 (includes EG:10775), RPP21, RPP30, RPP38, RPP40, RRN3, SLC27A3, SLC27A6, SMC6, SPARCL1, SRSF11, THAP11, TTI2 (includes EG:100334230), TUFT1, UBC, WDR3 | 24 | 16 | Developmental disorder, hereditary disorder, metabolic disease |
| Akt, c-Src, CCL20, CXCL1, CXCL10, CXCL11, CXCL13, ENSA, ESM1, EXOC4, Fgfr, HN1, HPGD, IκB kinase, IFN, gamma IFN, Ikb, IL-23, IL-17f dimer, IL17a dimer, IL17R, Integrin, IRAK4, JINK1/2, Lfa-1, MTORC2, NCAM1, NFκB (family), NfkB1-RelA, PI3K (family), Ptk, RAP2A, RIPK2, TLR9, Tlr | 22 | 15 | Cell-to-cell signaling and interaction, cellular movement, immune cell trafficking |
a
MHC, major histocompatibility complex; IKK, IκB kinase. Scores for each network were computed by ingenuity pathways analysis according to the fit of that network to the user-defined set of focus genes. Scores are derived from P values and indicate the likelihood of the focus genes in a network being found together due to random chance. A score of 2 indicates that there is a 1 in 100 chance that the focus genes are together in a network due to random chance. Therefore, scores of 2 or higher have at least a 99% confidence of not being generated by random chance alone.