Table 5. Comparative results for PATHOME (P), DAVID (D), GSEA (G) and MinePath (MP) in terms of selected pathways with reference to nine gold standard cancer-related pathway categories (see text for more details); PI3K –phosphoinositide-3-kinase; RTK–protein-tyrosine kinase; RB–retinoblastoma; HIF1 –hypoxia inducible factor; APC–antigen-presenting cell; GLI–glioma-associated oncogene; ‘✔’ identified as significant.
| Cancer PW categories | KEGG PW code | Pathway name | PATHOME | DAVID | GSEA | MinePath |
|---|---|---|---|---|---|---|
| PI3K | hsa04010 | MAPK signaling | ✔ | ✔ | ||
| PI3K, RTK | hsa04012 | ErbB signaling | ||||
| PI3K | hsa04062 | Chemokine signaling | ✔ | |||
| RB (Cell cycle) | hsa04110 | Cell cycle | ✔ | |||
| P53 | hsa04115 | P53 signaling | ✔ | |||
| HIF1, PI3K | hsa04150 | mTOR signaling | ✔ | |||
| Apoptosis | hsa04210 | Apoptosis | ||||
| APC | hsa04310 | Wnt signaling | ✔ | ✔ | ||
| GLI | hsa04340 | Hedgehog signaling | ||||
| SMAD | hsa04350 | TGF-β signaling | ||||
| PI3K | hsa04370 | VEGF signaling | ||||
| PI3K | hsa04510 | Focal adhesion | ✔ | ✔ | ✔ | |
| PI3K | hsa04910 | Insulin signaling | ✔ | |||
| HIF1, PI3K, RTK | hsa05200 | Pathways in cancer | ✔ | |||
| HIF1 | hsa05211 | Renal cell carcinoma |