Major/Minor Isoform And Tissue-Specific Expression

Question

[Pierre]

Hi,

I have a bunch of human genes id's from UCSC. I would like to do two things.

(1) I need to determine which transcripts of these genes are major / minor isoforms.

(2) I need to know where these transcripts are expressed - whether they are ubiquitously or tissue-specifically expressed.

Any pointer?

Thanks

edit: human genes

Answer 1

[Mikael Huss]

I'll assume human genes although this was not specified. For question (2), try:

BioGPS (microarray based)

Gene Expression Atlas (microarray/RNA-seq)

Gene Expression Baseline Atlas (several organisms; for human, data from Illumina BodyMap, ENCODE cell lines etc.)

UniGene - an oldie but goodie EST database

TIGER - Tissue specific gene expression and regulation

Pattern Gene Database

[Pierre]

Yes, human genes - edited. Thanks for these links, I think I will stick ot GEA or TIGER for the tissue-specificity. Any idea for the abundance of expression?

[Mikael Huss]

There is abundance information in BioGPS (where you can also download a table with raw data) and the Gene Expression Baseline Atlas (if you drill down a little bit); also check out RNA-seq Atlas (http://medicalgenomics.org/rna_seq_atlas/search), which also has a table with raw data, or GTex which has abundance info from RNA-seq but you have to register.

[cdsouthan]

I suspect these sources will give discordant results (http://cdsouthan.blogspot.se/2013/08/one-transcript-rules-ok.html)

Perhaps you could post how you got on with this challenge