Question: Transform from uniprot accesion to entrez gene id
0
gravatar for felipebihaiek
15 months ago by
felipebihaiek0 wrote:

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.

uniprot biocluster david entrez R • 692 views
ADD COMMENTlink modified 14 months ago • written 15 months ago by felipebihaiek0
1
gravatar for theobroma22
15 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 15 months ago by theobroma221.1k

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

ADD REPLYlink written 15 months ago by felipebihaiek0
1
gravatar for theobroma22
15 months ago by
theobroma221.1k
theobroma221.1k wrote:

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.

ADD COMMENTlink modified 15 months ago • written 15 months ago by theobroma221.1k
1
gravatar for theobroma22
15 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 15 months ago by theobroma221.1k

The Entrez ID is of course 90527.

ADD REPLYlink written 15 months ago by theobroma221.1k
0
gravatar for felipebihaiek
15 months ago by
felipebihaiek0 wrote:

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

ADD COMMENTlink written 15 months ago by felipebihaiek0
0
gravatar for theobroma22
15 months ago by
theobroma221.1k
theobroma221.1k wrote:

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.

ADD COMMENTlink written 15 months ago by theobroma221.1k
0
gravatar for felipebihaiek
14 months ago by
felipebihaiek0 wrote:

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

ADD COMMENTlink written 14 months ago by felipebihaiek0

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

ADD REPLYlink written 14 months ago by genomax49k
0
gravatar for theobroma22
14 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 14 months ago by theobroma221.1k
0
gravatar for felipebihaiek
14 months ago by
felipebihaiek0 wrote:

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.

ADD COMMENTlink written 14 months ago by felipebihaiek0

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.

ADD REPLYlink written 14 months ago by genomax49k

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?

ADD REPLYlink written 14 months ago by theobroma221.1k

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

ADD REPLYlink written 14 months ago by felipebihaiek0

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?

ADD REPLYlink modified 14 months ago • written 14 months ago by theobroma221.1k

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

ADD REPLYlink written 14 months ago by felipebihaiek0
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