Skip to main content

Table 4 The top 15 pathway retrieved by FoPA, PADOG, CePa and SPIA for the colorectal cancer (GSE8671) dataset

From: FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods

FoPA

PADOG

Rank

KEGG pathway

KEGG ID

PFoPA

Rank

KEGG pathway

KEGG ID

PPADOG

1

Non-small cell lung cancer

05223

0.0064

1

RNA transport

03013

0.0001

2

Intestinal immune network for IgA production

04672

0.0194

2

Cell cycle

04110

0.0001

3

Aldosterone-regulated sodium reabsorption

04960

0.0194

3

p53 signaling pathway

04115

0.0001

4

Tight junction

04530

0.038

4

Progesterone-mediated oocyte maturation

04914

0.0001

5

p53 signaling pathway

04115

0.048

5

Colorectal cancer

05210

0.0001

6

Wnt signaling pathway

04310

0.05

6

Non-small cell lung cancer

05223

0.0001

7

Mineral absorption

04978

0.0679

7

Endometrial cancer

05213

0.01

8

Renin-angiotensin system

04614

0.067

8

Small cell lung cancer

05222

0.0299

9

Alzheimer’s disease

05010

0.07

9

Glioma

05214

0.0299

10

Vasopressin-regulated water reabsorption

04962

0.07

10

RNA degradation

03018

0.040

11

NF-kappa B signaling pathway

04064

0.07

11

Apoptosis

04210

0.040

12

Neurotrophin signaling pathway

04722

0.08

12

Prostate cancer

05215

0.040

13

Melanoma

05218

0.09

13

Prion diseases

05020

0.040

14

Colorectal cancer

05210

0.1

14

Gap junction

04540

0.050

15

Leukocyte transendothelial migration

04670

0.12

15

Pancreatic cancer

05212

0.050

    

  
    

28

Wnt signaling pathway

04310

0.2

CePa

SPIA

Rank

KEGG pathway

KEGG ID

PCePa

Rank

KEGG pathway

KEGG ID

PSPIA

1

Cell adhesion molecules (CAMs)

04514

0.009

1

Chemokine signaling pathway

04062

0.001

2

Taurine and hypotaurine metabolism

00430

0.009

2

Cell cycle

04110

0.001

3

Glycosylphosphatidylinositol (GPI)-anchor biosynthesis

00563

0.009

3

p53 signaling pathway

04115

0.001

4

Regulation of actin cytoskeleton

04810

0.009

4

ECM-receptor interaction

04512

0.001

5

Circadian rhythm

04710

0.009

5

Gap junction

04540

0.001

6

Neurotrophin signaling pathway

04722

0.009

6

Natural killer cell mediated cytotoxicity

04650

0.001

7

Alanine, aspartate and glutamate metabolism

00250

0.009

7

Fc gamma R-mediated phagocytosis

04666

0.001

8

Drug metabolism - other enzymes

00983

0.009

8

Cholinergic synapse

04725

0.001

9

Dilated cardiomyopathy (DCM)

05414

0.009

9

GABAergic synapse

04727

0.001

10

Wnt signaling pathway

04310

0.009

10

Regulation of actin cytoskeleton

04810

0.001

11

Fructose and mannose metabolism

00051

0.009

11

Aldosterone-regulated sodium reabsorption

04960

0.001

12

NOD-like receptor signaling pathway

04621

0.009

12

HTLV-I infection

05166

0.001

13

Autophagy – animal

04140

0.009

13

Prostate cancer

05215

0.001

14

Glycosphingolipid biosynthesis - lacto and neolacto series

00601

0.009

14

Systemic lupus erythematosus

05322

0.001

15

Arrhythmogenic right ventricular cardiomyopathy (ARVC)

05412

0.009

  

0.001

    

123

Wnt signalling pathway

04310

0.97

  1. 'Wnt signaling pathway' and 'colorectal cancer' pathways shown in bold are expected to be impacted in GSE8671 dataset. These pathways are among the top-ranked pathways found by FoPA