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Table 3 Pathway analysis of the literature-collected and network-predicted candidate genes, respectively

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

Database Pathway Bonferonni p-value Candidate genes involved in the pathway
Literature-collected candidate genes
KEGG Regulation of actin cytoskeleton 4.70E-06 ACTB, BRAF, CDC42, CFL1, CHRM3, EZR, FGD1, FGF9, FGFR1, FGFR2, HRAS, ITGB1, KRAS, MAP2K1, MAP2K2, MYL2, MYL9, PDGFA, PFN1, PPP1CA, PPP1CB, PXN, RAC1, RAF1, RHOA, RRAS, SOS1
REACTOME Muscle contraction 5.39E-06 DES, MYH3, MYL2, MYL3, TNNI2, TNNT2, TNNT3, TPM1, TPM3, TPM4, TTN
KEGG Focal adhesion 1.05E-05 ACTB, BRAF, CCND1, CDC42, COL1A2, COL2A1, COL5A1, FLNA, GRB2, GSK3B, HRAS, IGF1, ILK, ITGB1, MAP2K1, MYL2, MYL9, PDGFA, PPP1CA, PPP1CB, PXN, RAC1, RAF1, RHOA, SOS1, THBS4
REACTOME Signaling by PDGF 3.61E-5 COL1A2, COL2A1, COL5A1, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, PDGFA PTPN11, RAF1, SOS1, STAT3, THBS4
REACTOME Signaling by insulin receptor 7.02E-05 EIF4E, EIF4EBP1, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, RAF1, RPS6, RPS6KB1, SOS1
REACTOME Signaling by EGFR 0.0022 CDC42, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, PTPN11, PXN, RAF1, SOS1
PANTHER RAS pathway 0.0025 BRAF, CDC42, GRB2, GSK3B, HRAS, KRAS, MAP2K1, MAP2K2, RAC1, RAF1, RHOA, RRAS, SOS1, STAT3
KEGG Hypertrophic cardiomyopathy (HCM) 0.0035 ACTB, DES, IGF1, ITGB1, MYH7, MYL2, MYL3, TNNT2, TPM1, TPM3, TPM4, TTN
BIOCARTA Role of MAL in Rho-mediated activation of SRF 0.044 ACTA1, CDC42, MAP2K1, MAP2K2, RAC1, RAF1, RHOA
BIOCARTA IGF-1 signaling 0.0067 FOS, GRB2, HRAS, IGF1, MAP2K1, PTPN11, RAF1, SOS1
PANTHER Integrin signaling 0.0070 BRAF, CDC42, COL1A2, COL2A1, COL5A1, FLNA, GRB2, HRAS, ILK, ITGB1, KRAS, MAP2K1, MAP2K2, PXN, RAC1, RAF1, RHOA, RND2, RRAS, SOS1
KEGG Dilated cardiomyopathy 0.0099 ACTB, DES, IGF1, ITGB1, MYH7, MYL2, MYL3, TNNT2, TPM1, TPM3, TPM4, TTN
Network-predicted candidate genes
REACTOME Muscle contraction 2.71E-24 ACTN2, DMD, MYBPC1, MYBPC2, MYBPC3, MYH8, MYL1, MYL4, NEB, TCAP, TMOD1, TNNC1, TNNC2, TNNI1, TNNI3, TNNT1, TPM2, VIM
KEGG Hypertrophic cardiomyopathy (HCM) 9.68E-6 ACTC1, DMD, MYBPC3, TGFB1, TGFB2, TGFB3, TNNC1, TNNI3, TPM2,
PANTHER TGF-beta signaling pathway 1.07E-5 BMP2, LEFTY1, LEFTY2, LOC100271831, MAPK1, MAPK3, MSTN, NODAL, TGFB1, TGFB2, TGFB3
KEGG Dilated cardiomyopathy 2.35E-5 ACTC1, DMD, MYBPC3, TGFB1, TGFB2, TGFB3, TNNC1, TNNI3, TPM2