Having a list of human transcript expression data, is there a way to know if some specific transcripts are involved in a disease when over or under-expressed?
Scratching my head thinking about this request. "Diseases" (multi-genic say diabetes or hypertension) are probably a delicate balance of interaction of multiple genes (which likely change with time). If we add environmental factors, I doubt if it would be possible build a database such as this or even if one did what value it would have. Perhaps others have a different view.
In addition, it's an open question how many of these over/under expressed genes are "primary" disease causing/pathogenic and how many are secondary "downstream" cellular reactions/coping mechanisms.
I think a cellular interaction network is far too complicate to say "this is a pathogenic transcript".
I am aware it is a very broad question. Trying to make it simpler: I focus only on cancers (even if genomax's comment about multi-gene diseases would still apply here) and on transcripts not necessarily causing the disease ("primary" as WouterDeCoster suggested) but at least having its expression deregulated in patients suffering cancer.
Isn't that what "gene signatures" represent (e.g. PAM50 for breast cancer, Prostate cancer, brain cancers etc)?
Indeed, but I think (not completely sure) while this kind of expression marker idea has been around for cancer for some time now, the two papers I linked are probably the first two applied to genetic disorders.
Not yet, but probably in the near future:
Genetic diagnosis of Mendelian disorders via RNA sequencing
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
Interesting papers. Seems to be a "work in progress" topic indeed.
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