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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