Table 3

Top 10 KEGG pathways ranked by p-value for the top two modules in the three disease case studies
Disease Functional Modules (# gene) Map Title in KEGG # of genes mapped in the pathway Fisher P value
Acute leukemias Module #1: Leukemia module (n = 44) Huntington's disease(hsa05016) 6 <0.0001
Cell cycle(hsa04110) 5 0.00015
Chronic myeloid leukemia(hsa05220) 4 0.00021
Prostate cancer(hsa05215) 4 0.00045
Notch signaling pathway(hsa04330) 3 0.00092
Pathways in cancer(hsa05200) 6 0.00184
Measles(hsa05162) 4 0.00209
Neuroactive ligand-receptor interaction(hsa04080) 5 0.00465
Primary immunodeficiency(hsa05340) 2 0.00913
Endometrial cancer(hsa05213) 2 0.01948
Module #2: Immune module (n = 32) JAK-STAT signaling pathway(hsa04630) 12 <0.0001
B cell receptor signaling pathway(hsa04662) 8 <0.0001
Primary immunodeficiency(hsa05340) 8 <0.0001
Measles(hsa05162) 7 <0.0001
Natural killer cell mediated cytotoxicity(hsa04650) 7 <0.0001
Osteoclast differentiation(hsa04380) 6 <0.0001
Hematopoietic cell lineage(hsa04640) 5 <0.0001
T cell receptor signaling pathway(hsa04660) 5 0.00012
Chemokine signaling pathway(hsa04062) 6 0.00019
Chronic myeloid leukemia(hsa05220) 4 0.00033
Lupus Module #1: Inflammatory Module (n = 69) MAPK signaling pathway(hsa04010) 28 <0.0001
Cell cycle(hsa04110) 12 <0.0001
Osteoclast differentiation(hsa04380) 15 <0.0001
Toll-like receptor signaling pathway(hsa04620) 16 <0.0001
NOD-like receptor signaling pathway(hsa04621) 14 <0.0001
GnRH signaling pathway(hsa04912) 12 <0.0001
Pertussis(hsa05133) 12 <0.0001
Leishmaniasis(hsa05140) 10 <0.0001
Chagas disease (American trypanosomiasis)(hsa05142) 11 <0.0001
Toxoplasmosis(hsa05145) 13 <0.0001
Module #2: Immune module (n = 49) Osteoclast differentiation(hsa04380) 13 <0.0001
JAK-STAT signaling pathway(hsa04630) 12 <0.0001
Measles(hsa05162) 10 <0.0001
Influenza A(hsa05164) 12 <0.0001
Pathways in cancer(hsa05200) 13 <0.0001
Hepatitis C(hsa05160) 8 <0.0001
Leishmaniasis(hsa05140) 5 <0.0001
Basal transcription factors(hsa03022) 4 0.00025
Toll-like receptor signaling pathway(hsa04620) 5 0.00028
Acute myeloid leukemia(hsa05221) 4 0.00033
Breast cancer Module #1: Proliferative module (n = 192) DNA replication(hsa03030) 16 <0.0001
Nucleotide excision repair(hsa03420) 13 <0.0001
ErbB signaling pathway(hsa04012) 15 <0.0001
Cell cycle(hsa04110) 41 <0.0001
Pathways in cancer(hsa05200) 28 <0.0001
Renal cell carcinoma(hsa05211) 13 <0.0001
Pancreatic cancer(hsa05212) 13 <0.0001
Chronic myeloid leukemia(hsa05220) 16 <0.0001
Focal adhesion(hsa04510) 20 <0.0001
Measles(hsa05162) 14 <0.0001
Module #2: Metastasis module (n = 74) Focal adhesion(hsa04510) 17 <0.0001
ECM-receptor interaction(hsa04512) 15 <0.0001
Amoebiasis(hsa05146) 11 <0.0001
Pathways in cancer(hsa05200) 14 <0.0001
Protein digestion and absorption(hsa04974) 8 <0.0001
Small cell lung cancer(hsa05222) 7 <0.0001
Bladder cancer(hsa05219) 4 0.00019
Malaria(hsa05144) 4 0.00041
Rheumatoid arthritis(hsa05323) 5 0.00041
Cytokine-cytokine receptor interaction(hsa04060) 8 0.00042

Ding et al.

Ding et al. BMC Genomics 2012 13:325   doi:10.1186/1471-2164-13-325

Open Data