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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