Pathway Database
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10.9 years ago
Elisa ▴ 80

Dear All

I'm studying a TM receptor protein. Do you know a pathway database where I could perfom a search by fasta sequence or receptor name to get all pathways in which my protein is involved?

Thanks

pathway • 5.0k views
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10.9 years ago

Pretty much any pathway database would allow you to do at least one of the two. Assuming that you are talking about a human protein involved in signal transduction, here are a few of the more relevant pathway databases to try:

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10.9 years ago

[?]

http://www.bioinformatics.fr/resources.php?tag=pathways [?]Try to use a specific ID for your receptor like his Entrez Gene Id or his Ensembl Id.[?]

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10.9 years ago
Thaman ★ 3.3k

There are lots of Pathway database tool but my preference goes to Reactome. From website you can do Pathway broswer, Pathway Analysis, Species comparison and Expression Analysis of eithe protein and encoded genes.

They have cross-reference wth NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

The rationale behind Reactome is to convey the rich information in the visual representations of biological pathways familiar from textbooks and articles in a detailed, computationally accessible format.

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Russh ★ 1.2k

Netpath might be of interest http://www.netpath.org/ But I'd say KEGG is your best start - it can be linked to from the entrezgene page for your gene R, treating pathway annotations with a pinch of salt since 2006

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10.9 years ago

This could be a bacterial protein - in which case EcoCyc is a good choice. Could be a plant protein and so one may need a specialized pathway database for plants, eg here. The other responses are good - I'm just offering other sources of info.

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