I am trying to extract some cell-specific transcriptomic/proteomic data for cancerous tissues from Human Protein Atlas, however, it did not work out. I appreciate any cues in doing so, and if there are other web resources for eliciting such data (except NCI-60), I appreciate even more.
www.proteinatlas.org/
Hi
You look for your gene by searching its symbol in search txt box in first page then choose best record and open its corresponding page. In result page you can see some photos of cells which have the expressed gene in microscopic lvl and after that you can see a chart which contain the expression of the gene in different organ and its protein localization features in those organs.
for example look at the following link which gives you those info about COX8A in different organs.
http://www.proteinatlas.org/ENSG00000176340-COX8A/tissue
but about other db, of course there some good other db like
https://www.ebi.ac.uk/gxa/home
and also
http://biogps.gnf.org/
BR
Ehsan
Dear Ehsan,
Thanks for your detailed response. In fact, I am looking for gene expression (transcriptomic) and proteomic "profiles" of specific tissues (exclusively for cancerous cells), not a single gene.
Nevertheless, I appreciate the useful resources you provided.
Kindly regards.
Hi Oveis,
I feel your pain. I too am interested in the expression levels of a group of proteins in tissues/cells throughout the body. This is similar in concept to your goal. Whilst there are numerous databases out there that allow you to look up individual proteins, I am yet to find one that will let me look up a group of proteins, or display expression profiles for a given tissue. The really annoying thing is that the data is there in these databases!! You just have to get it out. You can download some of these databases and I'd imagine with a tame bioinformatician it wouldn't be that difficult to extract what you require. But who has one of those? I find this really frustrating....
Dear Peter,
I agree with you. Recently, I came across this idea that the best way to find such data is literature surveying. While there are many other useful databases for such data, this database (Human Proteome Atlas) benefits from new extracted data (in contrast to NCI-60 project), as well as protemic data for a wide variety of cancerous tissue. Employing genome-scale metabolic models (in case of studying metabolism), would assist in assessment the interactions of "some particular" genes or their corresponding proteins through GPR associations.
However, there are two other useful resources for extracting such data: https://icgc.org/ and https://tcga-data.nci.nih.gov/tcga/ .
I hope we tackle this problem soon!
Best regards,
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