Table 3 Top 10 KEGG pathways ranked by p-value for the top two modules in the three disease case studies
From: atBioNet– an integrated network analysis tool for genomics and biomarker discovery
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 |
| Â | Â | 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 | |
| Â | 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 |
| Â | Â | 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 | |
| Â | 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 |
| Â | Â | 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 | ||
| Â | Measles(hsa05162) | 14 | <0.0001 | |
Module #2: Metastasis module (n = 74) | Focal adhesion(hsa04510) | 17 | <0.0001 | |
| Â | 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 |