Table 1.
Signaling pathways enriched for CCGs
| Signaling pathways and cellular processes | Percent tumor | Number CCG (GKC method) | P value | Number CCG (gCIS method) | P value | Representative genes | Analysis platform |
| Molecular mechanisms of cancer | 100 | 13 | 2.25E-06 | 35 | 8.79E-07 | Crebbp, Gsk3b, Mll3, Pten, and Nsd1 | IPA |
| GO:0016568− chromatin modification | 100 | 14 | 3.52E-05 | 34 | 3.26E-08 | Kdm6a, Mll3, Mll5, Myst3, and Nsd1 | DAVID |
| TGF-β | 90 | 7 | 3.46E-06 | 16 | 1.5E-06 | Acvr2a, Crebbp, Smad2, Smad4, and Smurf2 | IPA |
| RAR activation | 90 | 9 | 5.72E-06 | 21 | 1.27E-05 | Ncor1, Nsd1, Pdpk1, and Pik3r1 | IPA |
| HGF signaling | 90 | 7 | 1.12E-05 | 21 | 7.69E-09 | Atf2, Dock1, Grb2, Ptk2, Ptpn11, and Rap1a | IPA |
| ERK/MAPK | 90 | 8 | 8.89E-05 | 19 | 2.84E-04 | Grb2, Mapk1, Pak1, and Ptk2 | IPA |
| Tight junction signaling | 90 | 8 | 1.25E-03 | 17 | 9.91E-05 | Ash1l, Ctnna1, Inadl, Magi1, and Magi2 | KEGG |
| GO:0003682− chromatin binding | 90 | 9 | 6.6E-03 | 22 | 3.04E-05 | Adnp, Arid4b, Gata6, Mbd1, and Ncoa1 | DAVID |
| PI3K/Akt | 86 | 7 | 3.72E-05 | 15 | 2.14E-04 | Mapk1, Pdpki, Pik3ca, Pten, and Rps6kb1 | IPA |
| Integrin | 86 | 8 | 1.48E-04 | 23 | 1.39E-05 | Arhgap5, Itgb1, Ptk2, and Rapgef1 | IPA |
| Ephrin receptor | 86 | 7 | 3.7E-04 | 21 | 1.51E-05 | Abi1, Cdc42, Epha6, Gnaq, and Gna14 | IPA |
| Rac Signaling | 86 | 5 | 1.25E-03 | 15 | 5.29E-05 | Cdc42, Iqgap1, Iqgap2, Map3k1, and Pak1 | IPA |
| Formation of filaments | 81 | 10 | 6.75E-05 | 32 | 4.41E-05 | Akap13, Atxn2, Ctnnd1, and Fhit | IPA |
| Wnt/β-catenin | 76 | 5 | 1.02E-02 | 18 | 3.17E-04 | Csnk1d, Gnaq, Gsk3β, EP300, and Ppp2r5e | IPA |
| Adherens junction | 76 | 5 | 1.6E-02 | 15 | 7.42E-06 | Actn1, Cdh1, Crebbp, Ctnna1, and Ctnnd1 | KEGG |
Analysis of CCGs using IPA, DAVID, and KEGG revealed several canonical signaling pathways and processes enriched for CCGs from SB-driven pancreatic tumors. Percent tumor is the proportion of tumors that had a mutation in at least one CCG found within the pathway; 48 GKC CCGs and 174 gCCGs were significantly enriched in canonical pathways identified by IPA. P values for pathway enrichment were adjusted for multiple testing using the Benjamini–Hochberg method for control of the false discovery rate.