Table 3 Top 5 networks impacted by SSc-associated CpG differential methylation

Cancer, endocrine system disorders, organismal injury and abnormalities

Akt, ARL4C, BEX2, C1GALT1C1, CASK, CCDC120, CDK16, CG, Cyclin A, DLG3, estrogen receptor, FGFR2, FLT4, FSH, GALNT18, GFRA1, GRB10, Growth hormone, H19, HMGB3, Lh, MAGI1, MEST, mir-335, MPL, NAV1, NFYA, PARD6G, PAX8, PORCN, Proinsulin, Rb, TMEM204, YAP/TAZ, ZNF232

Developmental disorder, gastrointestinal disease, organismal injury and abnormalities

ADAP1, Alp, BCR (complex), Creb, DOCK11, DUSP9, EPS8L1, ERK1/2, FGD1, FLNA, G6PD, GTPase, KCNQ1, KCNQ1OT1, MAP2K1/2, MBTPS2, MSN, OTUD5, OTUD7A, p70 S6k, Pdgf (complex), PDGF BB, phosphatase, PI3K (family), Pka, PP2A, PSMB2, RB1, RPS6KA6, Rsk, SH3BP2, SHARPIN, Shc, Srebp, transcription factor

Connective tissue disorders, hereditary disorder, organismal injury and abnormalities

26 s Proteasome, Actin, caspase, CD3, CHST7, DKC1, EGLN, EIF2S3, F Actin, FAM83H, GLI4, HCFC1, HISTONE, Histone h2a, Histone h3, Histone h4, Hsp70, Hsp90, IKBKG, Immunoglobulin, KLF2, NECAB3, NFkB (complex), NOC2L, Notch, PARP11, PI3K (complex), Rnr, TCR, TMEM121, TMEM14C, TRAPPC9, Ubiquitin, USP6, Vegf

Cancer, cell death and survival, organismal injury and abnormalities

ADRB2, BARX2, CADM2, CAMK1G, CIITA, CREB1, CREBBP, DDX39A, FAS, GNAS-AS1, HEIH, HOXB3, IFNG, IL32, iodine, NEXMIF, NR4A1, PAX8-AS1, Pde4d, PDHA2, PDK3, PRPS2, PSD4, RGS9BP, SETD7, SMARCA4, SMIM10L2B, TFAP2E, TMEM187, TP53, TRPM1, TULP4, ZFP41, ZMIZ1, ZXDA

Cardiac dilation, hereditary disorder, organismal injury and abnormalities

AIFM1, AMPK, BCOR, BRCC3, Calmodulin, calpain, CMC4, cytokine, DUSP22, EFNB1, EMD, ERK, GNAS, GOPC, IFN Beta, IgG, Igm, Insulin, Interferon alpha, Jnk, Mapk, Mek, Nfat (family), P38 MAPK, PGK1, Pkc(s), PTK, Ras homolog, Sapk, SLC6A8, SLC7A5, SRC (family), SSBP4, STAT5a/b, UNC93B1