Question: API for cells gene expression levels
0
gravatar for nikitavlassenko
8 months ago by
nikitavlassenko10 wrote:

I am developing an iOS app to show various data about any cell's type (currently immune cells), and need to find somewhere an API that would let me query a genome database to retrieve gene expression values mainly (but further down the road other data too). I know that there is an 'ImmGen' app on 'Apple AppStore', so they are somehow getting this data:

https://itunes.apple.com/us/app/immgen/id378703882?mt=8

ios database genome • 312 views
ADD COMMENTlink written 8 months ago by nikitavlassenko10
1

You are not going to find expression values in a genome database. You would need to look at a gene expression database for that information. For cancer datasets you could use cBioPortal API. Other general expression RNAseq data API from EBI.

Unrelated question: Were you able to get the 10x demutiplex to work? You did not follow-up on the last two threads.

ADD REPLYlink written 8 months ago by genomax59k

Yes, the question was linked, if I am not mistaken, to the one I also asked on stackexchange: https://bioinformatics.stackexchange.com/questions/4024/10x-illumina-demultiplexing-sample-sheet-issue/4046#4046

ADD REPLYlink written 7 months ago by nikitavlassenko10

Actually no, but I added the link to the 10X question

ADD REPLYlink written 7 months ago by nikitavlassenko10

Ok, I tried out EBI and I suppose I can use TPM values in my app. However, there are no mgi_symbols in the matrix returned, for instance: ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/data/atlas/rnaseq/studies/arrayexpress/E-GEOD-39230/solanum_tuberosum/genes.tpm.htseq2.tsv So, do I need then to use a second query to BioMart from the iOS app? Or can I still get gene symbols somehow? What are these gene ids: EPlSTUG00000000602?

ADD REPLYlink written 7 months ago by nikitavlassenko10

mgi_symbols are for mouse genes where are the link you are referring to above is for a potato dataset (mouse to potato - that is not going to work). You need to define scope of your query carefully.

ADD REPLYlink written 7 months ago by genomax59k

Yeah, ok, I mean gene symbols. Will see then. I just do not need anything (ensembl id, entrez id, whatever) but gene symbols.

ADD REPLYlink written 7 months ago by nikitavlassenko10

I just do not need anything (ensembl id, entrez id, whatever) but gene symbols.

That will only work well for model organisms (human, mouse etc). If you are going to limit your app to those species then you would be fine. Once you step away from these there are no standard gene symbols.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax59k
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