This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get the pathway-protein relationship?

Dears,

I have a list of proteins ("Entry" values from UniProt) and I want to get a list of pathways which those proteins participate in. (i.e I need to match for each protein the pathway(s) it is member in.) Could you please help me with that?

Thanks.

pathways proteins
• 2,811 views • link
updated by h.mon h.mon • written by ahmedmelmoselhy • ahmedmelmoselhy

What have you tried so far? It would be good to know so people don't recommend things you have already tried.

• 0 views • link
written by GenoMax GenoMax

Each protein will likely be involved in many different pathways

• 0 views • link
written by Kevin Blighe Kevin Blighe

I need to match for each protein the pathway(s) it is member in.

Precisely. If it is then OP wants that list of pathways.

• 0 views • link
written by GenoMax GenoMax

4 answers

You can try STRING DB. The give protein-protein interactions + KEGG pathway annotations

• 0 views • link
written by pixie@bioinfo pixie@bioinfo

Go to Pathway Commons. Paste your uniprot ID in search window.

Look at FAQ on the main page for other ways of searching.

• 0 views • link
written by GenoMax GenoMax

If you have a small number of entries, you can use the KEGG Mapper – Convert ID, then clicking at the corresponding KEGG accession will take you to a page with lots of information, including the pathways that protein is involved.

If you have a large number of entries, you can use the BioConductor packages GAGE and Pathview (together with an Org.db package) to convert UniProt to Entrez, then map the Entrez IDs to pathways.

• 0 views • link
written by h.mon h.mon

You also may try webgestalt that performs an Gene Set Enrichment Analysis (GSEA), and Network Topology-based Analysis (NTA).

• 0 views • link
written by Buffo Buffo

Log in to answer this question.

More posts like this