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.
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".
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.