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markziemann / gmea

Gene Methylation Enrichment Analysis
MIT License
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Weird irrelevant pathways #16

Closed markziemann closed 7 months ago

markziemann commented 8 months ago

Sometimes LAM gives irrelevant results, for example olfactory receptors in muscle. These could be real signatures, but as these genes are probably not expressed in the muscle, they don't have any biological significance. One way to combat these irrelevant pathways is to remove genes that are not expressed in the tissue of interest. GTEX or human proteome atlas can be used to make a list of genes expressed in muscle and then we can conduct GMEA just on this list of genes.

markziemann commented 8 months ago

Thanks to Mandy and Sev for raising this issue.

markziemann commented 7 months ago

This issue would affect all methylation based enrichment analyses and so we won't mention it in the manuscript unless it is raised by the reviewers