Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.

Question

[michealsmith]

There can be multiple transcripts for one gene due to alternative splicing. I'm always curious about if different transcripts(of the same gene) will be tissue-specific. UCSC genome has heatmap for microarray expression among various tissues, which I think are generally for all transcripts, not telling if any tissue-specific expression difference for different transcripts of the same gene. So any recommended database?

thx

Answer 1

[Lynxoid]

You might want to try SHARQ to get a list of RNA-seq experiments that belong to a specific tissue, and then try to cross-reference that with expression database like GEO.

Answer 2

[Alex Paciorkowski]

I think a place you may want to start is the Gene Expression Omnibus. Within, some (not all) datasets may have the tissue-specific data you are looking for. I think though, a lot of the best data are really like to be from RNASeq, not expression arrays. But this might be a place to start.

[michealsmith]

Thanks. Then where can I find some RNA-seq database? Point here is to find tissue-specific expression difference for different "splicing transcripts", no matter what database used.

Answer 3

[Houkto]

I would also suggest Array express, although there is no tissue search but you can try to use the condition search instead.

Answer 4

[cdsouthan]

The answer has to be no. AFAIK there are no public probe sets with extensive results that have AS specificity. There are publications for such experiments but these (have to) use designed AS-specific PCR probes or specifically identify them by RNAseq reads