Table 1

30 top-ranked KEGG pathways using a prior probability of 0.05
KEGG pathway Number of genes Posterior probability of being included in the model Odds ratio Variance per gene (10^-3)
ABC transporters 24 1 Infinity 4.24
Lysosome 90 1 Infinity 3.56
Proteasome 40 1 Infinity 3.53
Complement and coagulation cascades 53 1 Infinity 3.13
RIG-I-like receptor signaling pathway 44 1 Infinity 2.80
ECM-receptor interaction 63 1 Infinity 2.59
Cell adhesion molecules (CAMs) 95 1 Infinity 2.50
Axon guidance 79 1 Infinity 2.46
SNARE interactions in vesicular transport 31 1 Infinity 2.39
RNA degradation 49 1 Infinity 2.39
Ubiquitin mediated proteolysis 105 1 Infinity 2.34
Neuroactive ligand-receptor interaction 125 1 Infinity 2.27
PPAR signaling pathway 58 1 Infinity 2.16
Ribosome 76 1 Infinity 2.15
MAPK signaling pathway 179 1 Infinity 2.11
Aminoacyl-tRNA biosynthesis 34 1 Infinity 2.08
Endocytosis 139 1 Infinity 2.08
Fc gamma R-mediated phagocytosis 70 1 Infinity 2.00
Insulin signaling pathway 97 1 Infinity 1.88
Cell cycle 96 1 Infinity 1.85
Notch signaling pathway 31 1 Infinity 1.73
Cytokine-cytokine receptor interaction 115 1 Infinity 1.69
Chemokine signaling pathway 138 1 Infinity 1.58
Metabolic pathways 793 1 Infinity 1.47
Tight junction 97 0.938 288 1.11
Purine metabolism 117 0.927 240 1.16
Chronic myeloid leukemia 58 0.919 215 1.27
Pathways in cancer 227 0.847 105 0.945
Basal transcription factors 23 0.826 90.3 1.28
Circadian rhythm - mammal 5 0.590 27.4 1.77

“Odds ratio” indicates the odds ratio between the prior and posterior probability of being included in the model. “Variance per gene” means the estimated variance of the t-statistic per gene. The gene sets are ranked primarily according to the posterior probabilities and secondarily according to the variance per gene.

Skarman et al.

Skarman et al. BMC Bioinformatics 2012 13:73   doi:10.1186/1471-2105-13-73

Open Data