EnrichmentMap - show in pathway commons Functionality - Better documentation needed

[risserlin]

Hard to figure out what is happening when you click on the "EnrichmentMap - show in pathway commons Functionality" in the network vs. in the heatmap. From playing around with this functionality these are my assumptions:

Click on "EnrichmentMap - show in pathway commons Functionality" from the network will search pathway commons for the name of the pathway for example - "SUPERPATHWAY OF CHOLESTEROL BIOSYNTHESIS%HUMANCYC%PWY66-5".

• If that pathway is found in pathway commons it will show it.
• If it is not found then it will show the best match that it has to that pathway.
• If the pathway is a parent pathway (if it is just a collection of sub-pathways) then it will show one of the subpathways. Not sure how that pathway is chosen though.

Click on "EnrichmentMap - show in pathway commons Functionality" from the heatmap will search pathway commons for the set of genes that are currently being displayed in the heatmap.

• this is really hard to align though as it could be any random pathway. There is a disconnect between what is searched for and what is being displayed because we can't actually see which genes were matched from the initial query.

[risserlin]

This wouldn't be needed, I think, if what was being searched for is transparent. If #481 was implemented I think this would be solved.