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Table 3 Top five networks influenced by CpG differential methylation

From: Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

Network Molecules in Network Score Focus Molecules
Embryonic Development, Organismal Development, Reproductive System Development and Function AGO2, AP2A2, BOP1, CACHD1, CENPS/CENPS-CORT, CEP120, Ck2, CSNK1D, CSNK1E, ESR1, FAAP20, FAM83D, FAN1, FBXW11, FGFR1OP, HPCAL1, Hsp70, INPP5B, KTN1, MAP3K9, mir-363, NIN, phosphatase, PPFIBP1, PSD4, RAPGEF5, RBM19, RNF166, Rnr, SAMD11, Smad2/3, Ubiquitin, UMODL1, USP2, WRAP73 52 29
Cancer, Connective Tissue Disorders, Organismal Injury and Abnormalities Akt, ANKRD11, CEACAM3, CHIA, COL23A1, COL4A1, COL5A1, collagen, Dynamin, Eph Receptor, EPHA1, EPHA10, GNB1L, GTPase, HOOK2, JINK1/2, KIAA1217, KIF26B, KSR1, Laminin (family), LIMS1, MAGI1, MTORC2, NAV1, NCK, NCK2, PARVB, PBXIP1, PI3K p85, PRDM16, PTPRN2, RPTOR, SH3BP4, SH3PXD2B, SH3RF3 42 25
Cell Morphology, Cellular Assembly and Organization, Cellular Development BCAR3, CK1, CLEC4C, DNAJC2, ERK1/2, Fgf, FXN, GALNT2, GSPT1, Hdac, HSP, HSPA12B, KCNN2, KCNN3, KCNQ3, LIN54, MARCH1, MHC Class II (complex), MYL12A, Ngf, NTF3, PLC gamma, potassium channel, Ral, RALGDS, ROBO1, ROR2, SH3BP2, SLC7A8, TFDP1, TUSC3, Vla-4, Wnt, WNT9A, histone deacetylase 35 22
Gene Expression, Connective Tissue Disorders, Immunological Disease CBS/CBSL, Ctbp, CTBP2, ETV6, GATAD2B, GPC6, Growth hormone, HDAC4, HDL-cholesterol, hemoglobin, HIPK2, HISTONE, Histone h4, Immunoglobulin, Jnk, KCNJ6, LDL, LDL-cholesterol, MECP2, MTHFD1L, N-cor, NCOR2, NFATC1, NPC2, Nr1h, NTM, PF4, Pias, PON1, POU2F1, SBNO2, STAT5a/b, TTC39B, VSX1, ZBTB16 33 21
Developmental Disorder, Hereditary Disorder, Organismal Injury and Abnormalities Alpha tubulin, ANO1, ATP11A, ATP5MC2, BETA TUBULIN, caspase, Cyclin E, DLGAP1, DLGAP2, DYSF, ERK, FMN1, FTSJ1, Hsp27, Hsp90, Insulin, KCNG2, MAP3K20, Mek, NLRP12, NNAT, p70 S6k, PACRG, PARP, Pde, PDE9A, PIWIL1, Ppp2c, PRKN, Proinsulin, RGPD4 (includes others), Sos, TRPV2, XAF1, ZBTB17 31 20