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Table 3 Cellular processes enriched in pancreatic mutated genes

From: Extending pathways and processes using molecular interaction networks to analyse cancer genome data

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
  1. 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.