How to get the pathway-protein relationship?
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2.6 years ago

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 • 789 views
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You could try KEGG pathway: https://www.genome.jp/kegg/pathway.html

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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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I found some paper mentioning Reactome [https://www.reactome.org/], I tried it but I couldn't get it.

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Each protein will likely be involved in many different pathways

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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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2.6 years ago
pixie@bioinfo ★ 1.4k

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

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2.6 years ago
GenoMax 107k

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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2.6 years ago
h.mon 33k

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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2.6 years ago
Buffo ★ 1.9k

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

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