8.5 years ago by
Boston MA area
"From a biological view point" I would say I would want to know about the spatial/temporal expression patterns of the transcripts/protein that carry the alteration. That said, I can imagine in some types of proteins it wouldn't matter much. In others if it was in a domain with key functionality, or impacted folding issues, it could matter a lot.
"longest transcript" Yeah, I would think it was fine to describe it in the context of the longest transcript if you are trying to orient people. But I might consider choosing the UCSC "canonical" or maybe a reference one from CCDS or Gencode or something? Or the way MapViewer or SeatteSNPs does it so it compresses/flattens all transcripts to a reference diagram--knowing that may not really represent a version that is actually used. As long as it's clear which way you decided to go and there's a reason for it, it would make sense. But I guess I would want to know what is the most common transcript too--longest is not necessarily the most common--could even be rare. A gene I worked on in grad school was like that. And we also had a different long transcript version that was long because of a 3' UTR--not a coding piece.
I think if I was asked to consider a gene with splice variants I'd want a diagram like the GVS gives, with SNPs and transcripts--and you can assess for yourself which SNPs would impact which transcripts:
"assess the effect" would bring me back to tissue/cell type/time point, possible interaction partners, etc.
Tools: this SIFT page (http://sift.jcvi.org/ ) also links to some other tools on the left side that I'd try. Maybe PMut too (http://mmb.pcb.ub.es/PMut/ )
Is that the sort of stuff you were looking for? Or you were just looking for computational answers? My PhD was on a muscle splice variant in a cell biology lab and I think like a cell biologist on that....
8.5 years ago by
Mary ♦ 11k