How to get the pathway-protein relationship?

Question

[ahmedmelmoselhy]

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.

[pltbiotech_tkarthi]

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

[GenoMax]

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

[ahmedmelmoselhy]

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

[Kevin Blighe]

Each protein will likely be involved in many different pathways

[GenoMax]

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.

Answer 1

[pixie@bioinfo]

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

Answer 2

[GenoMax]

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

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

Answer 3

[h.mon]

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.

Answer 4

[Buffo]

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