Transform from uniprot accesion to entrez gene id

Question

[felipebihaiek]

Hi I am currently trying to transform from uniprot accession to entrez gene id using david but I am obtaining an error as if the accession number where not recognized (for example if i submitENSP00000371650 as an accession). I have also tried using the mygene package in R but it seems it can only pass from gene ids to accession not the other way around. Any help will be appreciated. Thank you for reading.

Answer 1

[theobroma22]

Is this what you are looking for? A: get the uniprot accession from ensembl protein ID

[felipebihaiek]

Thang you but not I want the entrez(pubchem) gene id not the uniprot ones.

Answer 2

[theobroma22]

Once you open the link to uniprot in the answer I pasted for you, you can easily spin the wheel to the Entrez id for the output, or the To option.

Answer 3

[theobroma22]

Tying up loose ends: https://www.ncbi.nlm.nih.gov/gene/90527

[theobroma22]

The Entrez ID is of course 90527.

Answer 4

[felipebihaiek]

Okey this should work, but is the same case as in david I try converting ENSP00000267803 and get nothing as a result. ANY IDEAS?

Answer 5

[theobroma22]

Your gene of interest is not mapped. If your job was not successful and you are not sure whether you have selected the correct source database, try a text search in UniProtKB with one of your identifiers and look at an example entry. Check out the cross-reference section to find out which database uses this identifier. I don't see an Enterez cross reference ID for the ensembl ID above, but I do see a refseq ID and other IDs.

Answer 6

[felipebihaiek]

Thank you i do not know if to start a new thread, but once i get the GeneID i try to use the pug rest to find some properties of the proteins. For example y look at this

https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/xref/GeneID/856503/property/MolecularFormula/JSONP?callback=my_callback

the geneid 856503 does exist in NCBI but i can not manage to get any properties out using pug REST

[GenoMax]

Use the New Post button at the top right corner of any page to start a new thread.

Answer 7

[theobroma22]

Is this your gene of interest? https://www.ncbi.nlm.nih.gov/gene/?term=856503

Answer 8

[felipebihaiek]

Yes it is that one but i would like to use pug rest, as i am intereste in finding the assay id and its date in order to establish de discovery date for the bioactivity.Thank you.

[GenoMax]

Please use ADD REPLY/ADD COMMENT to respond to existing posts to keep threads logically organized. This response should be against @theobroma22's answer above.

[theobroma22]

I'm not quite sure what you are doing, or what pug rest is doing so why are you putting a gene ID into a substance database? You need to use a substance ID, right?

[felipebihaiek]

hi not really https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html if you see you can access via crossreference

[theobroma22]

Ok. This would tell me that this gene isn't involved in a metabolic pathway, or makes a substance. That is, it's a protein and not an enzyme. The NCBI link to the gene above states that it's involved with transport, or trafficking from the golgi to the cell wall, right?

[felipebihaiek]

not really what is happening is that pug rest is not founding the cross reference in the database