Does a database of pathogenic transcripts exist?

Question

[user31888]

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?

Thanks !

[GenoMax]

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.

[WouterDeCoster]

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".

[user31888]

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.

[GenoMax]

Isn't that what "gene signatures" represent (e.g. PAM50 for breast cancer, Prostate cancer, brain cancers etc)?

[h.mon]

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.

Answer 1

[h.mon]

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

[user31888]

Interesting papers. Seems to be a "work in progress" topic indeed.