Is There Any Website To Get Cellular Location Information For A List Of Genes?

Question

[Diwan]

Hi,

I have a list of 1000 genes and I would like to add the localization information as to whether they are membrane bound, cytosolic, extracellular or secreted. Is there any website or bioconductor package in which I can just submit the list of genes and get the information?

I checked the GO cellular component. But many genes have all terms such as cytoplasm, membrane, extracellular matrix etc. Is there a way to assign one cellular component term to each gene?

Any suggestion will be helpful.

Thanks

Diwan

[Neilfws]

Which organism?

[Diwan]

looking for humans. Thanks. -D

Answer 1

[David Westergaard]

Ah, there are multiple ways to get about this.

1. Uniprot If you're working on a model organism there's a good chance the gene product will have a Uniprot entry. You can use the API to retrieve records such as subcellular location (http://www.uniprot.org/faq/28#retrieving_entries_via_queries), or you can download a text dump of the page and parse it yourself (e.g. http://www.uniprot.org/uniprot/P02699.txt).

2. Prediction servers Certain prediction servers perform very well. Among these are TMHMM, SignalP. A good article on this: Olof Emanuelsson et al., Nature Protocols 2, 953-971 (2007).

[Diwan]

Thanks a lot. It is very useful. -Diw