I found a mutation in an alternative transcript of a human gene, which is not the main transcript – it is associated with a CDS, though. Correct me if I'm wrong, but usually RNA expression databases would rather give expression data at the gene level rather than at the transcript level, thereby making no difference between the various transcripts related to the gene of interest.
Now, I would like to determine the compared tissue-specific expression profile for the alternative transcripts of my gene of interest. Hopefully, this data would help me to draw a possible genotype/phenotype correlation and define the pathogenic mechanism of the disease.
Do you know any database which could provide me such a piece of information?
Which species are you working with? If it is human maybe you can take a look at RNA-seq data where you can see the expression of those exons that distinguish your alternative transcript from all the others in your gene. Maybe you could use the ENCODE project RNA-seq data.
Thanks Marta. Yes, indeed, I work on human species. That's an interesting track. I wilI look at ENCODE data (http://genome.ucsc.edu/encode/) and see if they are easy to handle.
I've just found an interesting tool: http://medicalgenomics.org/rna_seq_atlas
In my case, however, it didn't enable me to get data for the alternative transcript. I keep searching.
Here's an idea of the tool/databse I'm looking for: http://bioinformatica.uniroma2.it/DBATE/
Hi there,
There is this older database derived from analysis of ESTs where you can search for isoforms of your gene of interest and see the tissue of origin of the ESTs and compare their abundance (http://www.imm.fm.ul.pt/exonmine/index.php). It obviously has limitations, but depending on the isoform you are looking for, ESTs may be more informative than short RNA seq tags.
Hi Margarida.
You're right about the ESTs. It's an excellent idea. I should have thought of it, because it was a precious source of information before the chane of habbits brought by breakthrough of high throughput seqeuncing technologies.
You may try this one as well:
http://statgen.ncsu.edu/asg/
Good luck.
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