Question: subcellular localization human / Mouse / Rat
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gravatar for bzhtgb
7 months ago by
bzhtgb10
bzhtgb10 wrote:

Hi all, I try to annotate subcellular localization for all human, rat, mouse proteins. My goal is to add clear and simple information to manage (use a very limited vocabulary -example: secreted, transmembrane, cytosol, mitochondria, nucleus). I think I already performed a good annotation focused on secreted, using several db and papers. For the other localization, I'm going to look at eSLDB, LOCATE, comPPI.. Other possibility will be to used a predictor but ideally, I want to make a distinction between experimental evidence, prediction, inferred by homology, ... My goal is not to have a perfect thing at the end but to find easy sets of data to integrate, with a limited number of vocabulary/ cell compartment.

I know that is an old question, I find a similar post, with some good and usefull information but this post is 7 years olds.

Finally my question is , how do you manage localization in a simple way?

Best

localization protein • 225 views
ADD COMMENTlink modified 7 months ago by Arnaud Ceol750 • written 7 months ago by bzhtgb10
0
gravatar for Elisabeth Gasteiger
7 months ago by
Geneva
Elisabeth Gasteiger1.2k wrote:

Subcellular location information can be found in the UniProt Knowledgebase, in particular in the reviewed section UniProtKB/Swiss-Prot, as described in http://www.uniprot.org/help/subcellular_location The controlled vocabulary used for this is available at http://www.uniprot.org/locations/ (or http://www.uniprot.org/docs/subcell), and evidence is provided where possible (http://www.uniprot.org/help/evidences).

You can use the advanced search tool on the UniProt website http://www.uniprot.org to search by location and evidence.

ADD COMMENTlink written 7 months ago by Elisabeth Gasteiger1.2k
0
gravatar for Arnaud Ceol
7 months ago by
Arnaud Ceol750
Milan, Italy
Arnaud Ceol750 wrote:

You may check the Compartment database: http://compartments.jensenlab.org/ (this is a Stringdb's style database for sub cellular compartments).

ADD COMMENTlink written 7 months ago by Arnaud Ceol750
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