Table 4 Pathway analysis of the overall candidate gene list (literature-collected and network-predicted)

REACTOME

Muscle contraction

4.55E-33

ACTN2, DES, DMD, MYBPC1, MYBPC2, MYBPC3, MYH3, MYH8, MYL1, MYL2, MYL3, MYL4, NEB, TCAP, TMOD1, TNNC1, TNNC2, TNNI1, TNNI2, TNNI3, TNNT1, TNNT2, TNNT3, TPM1, TPM2, TPM3, TPM4, TTN, VIM

KEGG

Hypertrophic cardiomyopathy (HCM)

1.21E-9

ACTB, ACTC1, DES, DMD,IGF1, ITGB1, MYBPC3, MYH7, MYL2, MYL3, TGFB1, TGFB2, TGFB3, TNNC1, TNNI3, TNNT2, TPM1, TPM2, TPM3, TPM4, TTN

KEGG

Dilated cardiomyopathy

1.21E-8

ACTB, ACTC1, DES, DMD, IGF1, ITGB1, MYBPC3, MYH7, MYL2, MYL3, TGFB1, TGFB2, TGFB3, TNNC1, TNNI3, TNNT2, TPM1, TPM2, TPM3, TPM4, TTN

KEGG

Focal adhesion

4.68E-7

ACTB, ACTN2, BRAF, CAV1, CCND1, CDC42, COL1A2, COL2A1, COL5A1, FLNA, GRB2, GSK3B, HRAS, IGF1, IGF1R, ILK, ITGB1, MAP2K1, MAPK1, MAPK3, MYL2, MYL9, PDGFA, PPP1CA, PPP1CB, PRKCA, PXN, RAC1, RAF1, RHOA, SOS1, THBS4

REACTOME

Signaling by insulin receptor

3.83E-6

EIF4E, EIF4EBP1, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, RAF1, RHEB, RPS6, RPS6KB1, SOS1

KEGG

Regulation of actin cytoskeleton

4.29E-6

ACTB, ACTN2, BRAF, CDC42, CFL1, CHRM3, EZR, FGD1, FGF3, FGF9, FGFR1, FGFR2, HRAS, ITGB1, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, MYL2, MYL9, PDGFA, PFN1, PPP1CA, PPP1CB, PXN, RAC1, RAF1, RHOA, RRAS, SOS1

PANTHER

TGF-beta signaling pathway

7.01E-6

AMH, AMHR2, BMP2, BMP4, BMP5, BMP7, CDC42, FOS, FOXO1, FOXP3, HRAS, KRAS, LEFTY1, LEFTY2, MAPK1, MAPK3, MSTN, NODAL, RHEB, RRAS, TGFB1, TGFB2, TGFB3

BIOCARTA

Integrin signaling pathway

1.35E-5

ACTA1, ACTN2, CAV1, GRB2, HRAS, ITGB1, MAP2K1, MAP2K2, MAPK1, MAPK3, PXN, RAF1, RHOA, SOS1

REACTOME

Signaling by PDGF

7.27E-5

COL2A1, COL1A2, COL5A1, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, PDGFA, PTPN11, RAF1, SOS1, STAT3, THBS4

KEGG

Cardiac muscle contraction

0.0024

ACTC1, MYH7, MYL2, MYL3, TNNC1, TNNI3, TNNT2, TPM1, TPM2, TPM3, TPM4

PANTHER

RAS pathway

0.0030

BRAF, CDC42, GRB2, GSK3B, HRAS, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, RAC1, RAF1, RHOA, RRAS, SOS1, STAT3

KEGG

Vascular smooth muscle contraction

0.0058

ACTA2, BRAF, MAP2K1, MAP2K2, MAPK1, MAPK3, MYH11, MYL9, PPP1CA, PPP1CB, PRKCA, PRKCE, RAF1, RHOA