Table 3 Consolidated pathway representations, their similarity indexes, and links to visualize the merged networks in the PathMe Viewer. A detailed analysis with the scripts to replicate the results and comments on the identified overlaps for each of the 21 equivalent pathways is available at https://nbviewer.jupyter.org/github/PathwayMerger/PathMe-Resources/blob/master/notebooks/case_scenarios/evaluating_similarity_equivalent_pathways.ipynb
From: PathMe: merging and exploring mechanistic pathway knowledge
KEGG | Reactome | WikiPathways | Pathway Similarity Index |
|---|---|---|---|
Cell cycle | Cell Cycle | Cell Cycle | 0.70 |
Toll-like receptor signaling pathway | Toll-Like Receptors Cascades | Toll-like Receptor Signaling Pathway | 0.62 |
mTOR signaling pathway | mTOR signalling | Target Of Rapamycin (TOR) Signaling | 0.58 |
Hedgehog signaling pathway | Signaling by Hedgehog | Hedgehog Signaling Pathway | 0.56 |
Apoptosis | Apoptosis | Apoptosis | 0.43 |
IL-17 signaling pathway | Interleukin-17 signaling | IL17 signaling pathway | 0.42 |
PI3K-Akt signaling pathway | PI3K/AKT activation | PI3K-Akt Signaling Pathway | 0.42 |
Wnt signaling pathway | Signaling by WNT | Wnt Signaling Pathway | 0.41 |
MAPK signaling pathway | MAPK family signaling cascades | MAPK Signaling Pathway | 0.40 |
B cell receptor signaling pathway | B Cell Receptor Signaling Pathway | Signaling by the B Cell Receptor (BCR) | 0.37 |
Pentose phosphate pathway | Pentose phosphate pathway (hexose monophosphate shunt) | Pentose Phosphate Pathway | 0.33 |
Citrate cycle (TCA cycle) | Citric acid cycle (TCA cycle) | TCA Cycle | 0.33 |
Synthesis and degradation of ketone bodies | Ketone body metabolism | Synthesis and Degradation of Ketone Bodies | 0.33 |
Notch signaling pathway | Signaling by NOTCH | Notch Signaling Pathway | 0.29 |
DNA replication | DNA Replication | DNA Replication | 0.28 |
Prolactin signaling pathway | Prolactin receptor signaling | Prolactin receptor signaling | 0.28 |
TGF-beta signaling pathway | Signaling by TGF-beta family members | TGF-beta Signaling Pathway | 0.26 |
Thyroid hormone synthesis | Thyroxine biosynthesis | Thyroxine (Thyroid Hormone) Production | 0.20 |
Sphingolipid metabolism | Sphingolipid metabolism | Sphingolipid Metabolism | 0.16 |
Mismatch repair | Mismatch Repair | Mismatch repair | 0.08 |
Non-homologous end-joining | Nonhomologous End-Joining (NHEJ) | Non-homologous end joining | 0 |