Table 3.
Cellular processes enriched in pancreatic mutated genes
| Cellular Process database | Cellular process | ORA Q-value before/after extension | Pathway size before/after extension | Number of mutated genes in new pathway | Number of mutated genes among added genes | Mutated genes among added genes |
|---|---|---|---|---|---|---|
| Reactome | Hemostasis | 0.475/5.18e-06 | 221/278 | 19 | 4 | LRP1B, TFPI2 PON1, SIGLEC11 |
| KEGG | Tight junction | 1.48E-4/4.5e-05 | 106/126 | 14 | 3 | RASIP1, RASGRP3, PLEKHG2 |
| KEGG | MAPK signaling pathway | 3.35E-4/4.87e-05 | 225/279 | 21 | 6 | DOCK2, MAPKBP1, SLC9A5 RASIP1, DUSP19, PLEKHG2 |
| KEGG | Cell adhesion molecules | 2.87E-4/1.03E-4 | 109/116 | 12 | 2 | TNR, SEC14L3 |
| KEGG | Wnt signaling pathway | 3.35E-4/1.39E-4 | 123/147 | 14 | 3 | MAPKBP1, PLEKHG2, ANKRD6 |
| KEGG | Neuroactive ligand- receptor interaction | 3.35E-4/1.72E-4 | 198/217 | 17 | 3 | EML1, ACE |
| BioCarta | MAPKinase Signaling Pathway | 1.33E-3/2.89E-4 | 81/111 | 8 | 2 | MAPKBP1, DUSP19 |
| Reactome | Apoptosis | 3.7E-2/4.42E-4 | 124/146 | 11 | 2 | BCL2A1, RASGRP3 |
| Reactome | Signaling by PDGF | 5.72E-3/4.43E-4 | 61/121 | 10 | 3 | VPS13A, LIG3 FMR2 |
| BioCarta | Cell Cycle G1/S Check Point | 1.7E-3/5.06E-4 | 27/34 | 5 | 1 | TGIF2 |
| BioCarta | Agrin Postsynaptic Differentiation | 1.27E-2/8.21E-4 | 27/38 | 5 | 2 | PGM5, PLEKHG2 |
| BioCarta | p38 MAPK Signaling Pathway | 3.25E-3/1.13E-3 | 34/42 | 5 | 1 | PLEKHG2 |
| BioCarta | ALK in cardiac myocytes | 2.89E-3/1.25E-3 | 32/44 | 5 | 1 | TBX5 |
| KEGG | Fc epsilon RI signaling pathway | 2.69E-2/2.71E-3 | 67/114 | 10 | 5 | DOCK2, MAPKBP1, DUSP19, ATF2, RASGRP3 |
| KEGG | ErbB signaling pathway | 2.32E-2/3.52E-3 | 86/196 | 13 | 7 | VPS13A, MAPKBP1, NEK8, LIG3, DUSP19, AFF2, GLTSCR1 |
| KEGG | Regulation of actin cytoskeleton | 4.94E-3/2.72E-3 | 184/236 | 15 | 4 | RASIP1, CDC42BPA, PLEKHG2, CYFIP1 |
| BioCarta | HIV-I Nef negative effector of Fas and TNF | 7.88E-3/4.78E-3 | 50/66 | 5 | 1 | DUSP19 |
| KEGG | p53 signaling pathway | 5.62E-3/5.44E-3 | 59/64 | 7 | 1 | PPP2R4 |
| Reactome | Signaling in Immune system | 0.459/7.02E-3 | 228/266 | 12 | 1 | SEC14L3 |
The complete list of cellular processes that display a statistically significant enrichment in pancreatic cancer mutated genes after applying the proposed extension method (Q-value < 0.01) and improved significance scores in relation to the original pathways (i.e. Q-values decreasing after the extension). The significance scores for the overrepresentation analysis (ORA) and the pathway sizes are shown before and after the extension, and the total number of mutated genes in the extended pathways is provided, as well as the size and the annotations for the set of mutated genes among the genes that were added to these pathways.