Skip to main content

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.