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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
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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.

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written by GenoMax GenoMax

Each protein will likely be involved in many different pathways

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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.

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written by GenoMax GenoMax

4 answers

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

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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.

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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.

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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).

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written by Buffo Buffo

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