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"Dark matter" - explore genes not found in any of the genesets in the context of the enrichment map

Open risserlin opened this issue 9 years ago • 1 comments

Provided that the user has supplied an expression /rank file often there are genes that are highly differential but are not covered by any of the genesets that are present in the enrichment map. It would be nice if there was an option to view this set of genes in the expression viewer with the click of a button.

Only issue with doing this in the EM context is that p-values are generally not supplied for the gene expression set. There might be a rank file but it is difficult to associate a cut-off (like pvalue < 0.05) when only ranks are available. it would still be useful to be able to see all genes that are not covered within the expression viewer of the enrichment map.

Maybe even have them as a separate node in the top section of the enrichment so when doing post analysis they aren't excluded. - In this case we would really want to limit it to the set of genes that are significant and not part of any genesets.

risserlin avatar Jan 08 '16 16:01 risserlin

Add p-values for genes after the fact

mikekucera avatar Sep 27 '16 19:09 mikekucera