review module 3 lab 2 - gsea to EM

[risserlin]

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[risserlin]

updated screenshots and used updated date for module 3 gsea lab

updated the preselection of drug targets in the file as the genesets for two of the drugs had changed dramatically. One went from having ~20 genes to have 5 genes - verified that this was in fact the right set on drugbank website. I am not sure if something was wrong with our initial gmt file or if the set had changed that much. Two of the drugs had the exact same composition.

noticed an issue with a red set being connected to a blue set - can easily get rid of it with "filter by expression set" but then you loose some f the benefit of not filtering (consistency between EMs) --> kept it. Need to add explanation or tip box.

BMP receptor signaling is no longer part of a cluster. It is its own single node. --> played around with parameters to see if I can get the EM to have the clulster of BMP that we saw previously.