Question: Protein location by gene name
1
gravatar for carolinapr.rocha
3.5 years ago by
Brazil
carolinapr.rocha50 wrote:

 

I've got a list of codding genes and i would like to get the cellular location of the expressed proteins, all at once. I already looked up on uniprot but wasn't able to solve it.

 

ADD COMMENTlink modified 3.5 years ago by Elisabeth Gasteiger1.5k • written 3.5 years ago by carolinapr.rocha50
3
gravatar for Chris Evelo
3.5 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

You could use data from the human protein atlas or neXtProt for this.

 

ADD COMMENTlink written 3.5 years ago by Chris Evelo9.9k

Hi, thank you for your answer.

Can I upload my data over there or should I search gene by gene?

ADD REPLYlink written 3.5 years ago by carolinapr.rocha50
2
gravatar for David Westergaard
3.5 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

http://compartments.jensenlab.org allows you to look up each gene individually, or download a flatfile with the location of each.

ADD COMMENTlink written 3.5 years ago by David Westergaard1.4k
0
gravatar for carolinapr.rocha
3.5 years ago by
Brazil
carolinapr.rocha50 wrote:

Hi, thank you for your answer.

Can I upload my data over there or should I search gene by gene?

ADD COMMENTlink written 3.5 years ago by carolinapr.rocha50
1

I am not sure about Protein Atlas. We actually downloaded some of the data they use for our own TissueAnalyzer on WIkiPathways. So you definitely download the data and use it locally and do your own queries, but they might support online queries too. 

NeXtProt definitely offers a SPARQL endpoint (that was actually presented at a recent ISMB keynote) and might have other services to query it with the data you want to use. You might still prefer to download the data though.

 

ADD REPLYlink written 3.5 years ago by Chris Evelo9.9k
0
gravatar for Elisabeth Gasteiger
3.5 years ago by
Geneva
Elisabeth Gasteiger1.5k wrote:

If you want to use UniProt, you can use the "Retrieve/ID mapping" service to upload your list of identifiers (or gene names): http://www.uniprot.org/uploadlists

Select the appropriate value under "From:" (e.g. HGNC, Gene names, RefSeq), and choose to map to UniProtKB.

Once you have your result, you can use the "Columns" button to customize your output, and in particular to add a column for subcellular location (and optionally remove other columns). These customized results can then be downloaded in tab-delimited format. See also http://www.uniprot.org/help/customize

Please don't hesitate to contact the UniProt helpdesk if you have additional questions.

ADD COMMENTlink written 3.5 years ago by Elisabeth Gasteiger1.5k
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