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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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Painter app gene overlap very poor for supposedly identical pathways #442

Closed risserlin closed 2 years ago

risserlin commented 3 years ago

Not sure if this is a painter issue or an EM issues.

Right click on a pathway in EM (for example: INTERFERON GAMMA SIGNALING%REACTOME%R-HSA-877300.1) and launch in pathway commons which open the pathway commons beta painter app.

pathway commons lists a bunch a pathways that have overlap with the genes associated with this pathway.
issues: interferon gamma is not number one. (EGFR1 is). The closest match is interferon alpha/beta but there are only 3 genes that overlap with it? If I do the same search directly on the pathway commons interferon alpha/beta comes up first (but no indication of overlap because not the way the web version works.

jvwong commented 3 years ago

Here's what Dylan tried to prioritize search results in the Painter, and maybe you can see the edge cases:

  1. Let a gene set (i) be G_i and an set of expressed genes in that gene set be E_i.
  2. Group G_i into gene subsets of max size 15 and use these to query PC for pathways
  3. For each pathway (j) returned P_ij, get the set of genes for that pathway G_Pij
  4. Calculate the overlap O_ij which is the intersection between G_Pij and E_i
  5. Prioritize results by O_ij

The chunking of genes into search queries (2) may seem weird but it was a trade-off that we made to be able to accommodate some enormous gene sets that would cripple the search.