Table 1.
GeneGo pathways related to cell adhesion, cytoskeleton remodeling, epithelial–mesenchymal transition (EMT) and WNT/β-catenin signaling, in which epigenetically and genetically affected genes in gastric carcinomas belonging to Clusters A, B1 and B2 were significantly accumulated (FDR < 0.05)
| Category | Cluster A | Cluster B1 | Cluster B2 | |||
|---|---|---|---|---|---|---|
| Pathways | Involved gens | Pathways | Involved gens | Pathways | Involved gens | |
| Cell adhesion | E-cadherin signaling and its regulation in gastric cancer | ACTN2, TWIST1, WNT2, ACTA1, EGFR, CTNNA1, FZD2, ZEB2 | Cell adhesion_Histamine H1 receptor signaling in the interruption of cell barrier integrity | TLN2, CDH1, CTNNB1, PRKCD, ROCK1, ACTB, CTNNA3, MYLK, ITPR3, GNA15 | ||
| Cell adhesion_Role of CDK5 in cell adhesion | TLN2, CDH1, CTNNB1, CTNNA3, ERBB2 | |||||
| E-cadherin signaling and its regulation in gastric cancer | CDH1, CTNNB1, WNT16, ACTA1, CTNNA3, FZD10, TWIST1 | |||||
| Cell adhesion_Cadherin-mediated cell adhesion | CDH2, CDH1, CTNNB1, ACTB, ACTA1, CTNNA3 | |||||
| Cell adhesion_ECM remodeling | CXCR1, NID1, ACTB, FLOT2, MMP9, IGF2, ERBB4, COL4A1 | |||||
| Cell adhesion_Endothelial cell contacts by non-junctional mechanisms | CDH2, CTNNB1, ACTB, CTNNA3, COL4A1 | |||||
| Cell adhesion_Role of tetraspanins in the integrin- mediated cell adhesion | TLN2, CD53, ROCK1, ACTB, ACTA1, FLNA | |||||
| Cell adhesion_Endothelial cell contacts by junctional mechanisms | CDH2, CTNNB1, VIM, ACTB, CTNNA3 | |||||
| Cell adhesion_Integrin-mediated cell adhesion and migration | TLN2, MYLK, ROCK1, ACTB, COL4A1 | |||||
| Cytoskeleton remodeling | Cytoskeleton remodeling_Keratin filaments | ACTN2, TWIST1, WNT2, ACTA1, EGFR, CTNNA1, FZD2, ZEB2 | Cytoskeleton remodeling_Keratin filaments | PLEC, TUBB8, PKP2, EPPK1, VIM, ACTB, KRT1, KRT13 | Cytoskeleton remodeling_ Thyroliberin in cytoskeleton remodeling | TRHR, PRKCB, PRKAR1B, ADCY4, PLCB1, TRH |
| Cytoskeleton remodeling_Role of PKA in cytoskeleton reorganization | ROCK1, PRKAR1B, ADCY4, ACTB, MYLK, ITPR3, ADD2 | |||||
| Cytoskeleton remodeling_ Regulation of actin cytoskeleton organization by the kinase effectors of Rho GTPases | TLN2, PIP5K1A, ROCK1, ACTB, FLNA, SPTBN5, MYLK | |||||
| Cytoskeleton remodeling_ Thyroliberin in cytoskeleton remodeling | TRHR , CACNA1C, PRKAR1B, ADCY4, TRH, ITPR3 | |||||
| EMT | Development_Regulation of epithelial-to-mesenchymal transition (EMT) | IL1B, CDH2, CDH1, VIM, WNT16, MMP9, FZD10, ACTB, SKIL, TWIST1 | Development_ Regulation of epithelial-to- mesenchymal transition (EMT) | IL1B, CDH2 , VIM, WNT2, FGF2, FZD10, TWIST1, TNF | ||
| Development_TGF-β-dependent induction of EMT via RhoA, PI3K and ILK | CDH1, CTNNB1, VIM, ACTA1, ROCK1, ACTB | |||||
| Development_TGF-β-dependent induction of EMT via SMADs | CDH2, CDH1, VIM, SMAD4, TWIST1 | |||||
| WNT/β- catenin signaling | WNT signaling in gastric cancer | SKP2, SFRP1, SFRP2, APC, WNT8A, FZD2, WNT2, TNF | Development_Negative feedback regulation of WNT/β-catenin signaling | CTNNB1, PRKCD, RNF43, WNT16, HUWE1, TRRAP, FZD10 | ||
| Development_ Negative regulation of WNT/β-catenin signaling in the nucleus | FHIT, KDM2B, RNF43, PAX7, TLE4, RUNX3, VHL, WNT2, APC, SOX17, CTNNA1, FZD2, NOS3, YWHAZ | Development_Negative regulation of WNT/β-catenin signaling in the nucleus | RUNX3, FHIT, VHL, CTNNB1, PRKCD, RNF43, PAX7, WNT16, GLI3, TRRAP, FZD10 | |||
| Development_Negative regulation of WNT/β-catenin signaling in the cytoplasm | DAB2, CDH1, TP53, VHL, CTNNB1, WNT16, HUWE1, FZD10 | |||||
All statistically significant GeneGo pathways revealed by MetaCore software using epigenetically and genetically affected genes in gastric carcinomas belonging to Clusters A, B1 and B2 are shown in Supplementary Table S11, available at Carcinogenesis Online.