More Synthetic Networks (Pathway Databases)

[annaritz]

In addition to Panther pathways (#10, #11), we could also add signaling pathways from the KEGG pathway database, Reactome, or NetPath pathways (oldies but goodies, available from the wayback machine circa 2023).

Another option is to use WikiPathways, which includes collections from KEGG, NetPath, and other manually-curated pathway databases. We could focus on one signaling pathway (e.g., Wnt, or EGFR), and WikiPathways will return a set of pathways related to the search term.

This might not broaden the set of possible datasets/applications.

[ntalluri]

For the kegg pathways, if taken from PathwayCommons, I think they happen to all be metabolic pathways. I had a conversation about this with Tony about metabolic pathways not being a good source to use. (Except I don't remember all the details as to why). Sumedha's Master's capstone was using these specifically, if we need some code to look at.

[tristan-f-r]

WikiPathways also includes all of the Reactome pathways in their Reactome portal.