Question: Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
1
gravatar for michealsmith
6.3 years ago by
michealsmith740
michealsmith740 wrote:

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

transcript • 5.1k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 6.3 years ago by michealsmith740
2
gravatar for Lynxoid
4.3 years ago by
Lynxoid220
Pleasanton, CA
Lynxoid220 wrote:

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.

ADD COMMENTlink written 4.3 years ago by Lynxoid220
1
gravatar for Alex Paciorkowski
6.3 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

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.

ADD COMMENTlink written 6.3 years ago by Alex Paciorkowski3.3k

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.

ADD REPLYlink written 6.3 years ago by michealsmith740
1
gravatar for Houkto
6.3 years ago by
Houkto210
Houkto210 wrote:

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

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Houkto210
1
gravatar for cdsouthan
6.3 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

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 specificaly identify them by RNAseq reads

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by cdsouthan1.8k
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