4 weeks ago by
St. Louis, MO
Yeah, enrichment analysis has a bad tendency to be misused pretty frequently for just the reason you describe. If you show all of the tissues/organelles/pathways, it's less of an issue, as it's much more believable if the top 10 hits or whatever are all related. But if you harp on a singular outlier (e.g. golgi bodies when most of the other hits are related to the ECM/cell membrane), it becomes much more apparent that you're "cherry picking". This is especially true given the nature of enrichment analysis where 3-5 genes can be considered a significant enrichment depending on the term and the number of genes attached to it. In general, if you're just trying to show a general association with a given process/pathway/tissue-specificity, I think just showing the top x hits from your enrichment analysis is usually enough to get the point across, even if every single term/tissue isn't exactly what you want. Beyond much more than that, you'd best start tying in some experimental validations.
As for other options, the tissue-specific route is a pretty good one, though more labor and time intensive. As you mention, GTEx has a wide variety, and other resources like the Human Tissue Atlas and JENSEN Tissue Database give more experimental protein data. The Human Cell Atlas provides protein-validated cellular localization data that's pretty handy.