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

From: Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

Database Pathway Bonnferoni p-value Candidate genes involved in the pathway
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