Question: subcellular localization human / Mouse / Rat
gravatar for bzhtgb
3 months ago by
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?


localization protein • 149 views
ADD COMMENTlink modified 12 weeks ago by Arnaud Ceol750 • written 3 months ago by bzhtgb10
gravatar for Elisabeth Gasteiger
12 weeks ago by
Elisabeth Gasteiger1.1k wrote:

Subcellular location information can be found in the UniProt Knowledgebase, in particular in the reviewed section UniProtKB/Swiss-Prot, as described in The controlled vocabulary used for this is available at (or, and evidence is provided where possible (

You can use the advanced search tool on the UniProt website to search by location and evidence.

ADD COMMENTlink written 12 weeks ago by Elisabeth Gasteiger1.1k
gravatar for Arnaud Ceol
12 weeks ago by
Arnaud Ceol750
Milan, Italy
Arnaud Ceol750 wrote:

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

ADD COMMENTlink written 12 weeks ago by Arnaud Ceol750
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