subcellular localization human / Mouse / Rat

Question

[bzhtgb]

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

Answer 1

[Elisabeth Gasteiger]

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.

Answer 2

[Arnaud Ceol]

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