Need Help In Protein Protein Interaction
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9.2 years ago
rezwan.02 ▴ 40

Friends, I imputed a file containing 17 proteins in STRING database and found 10 more proteins having the probability to interact with those proteins. now my question is from an interaction between two proteins that i got from the STRING result, how can i found this interaction is related to to which pathway ?

interaction pathway • 2.2k views
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9.2 years ago
terdon ▴ 430

You can't. The best you can do is check if both interacting partners are part of the same pathway. However, you can have a pathway like the following:

A => B => C

If you find an interaction between A and C, you have no way of knowing if that interaction has anything to do with the pathway that they are both associated with. Perhaps this interaction happens in another tissue, or at a different time.

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9.2 years ago
enunvillafer ▴ 100

you can use reactome database to search for the pathways in which the 17 proteins and their interacting partners participate. then you can see in the resulting pathways which proteins are connected directly in a given pathway or which proteins belong to the same pathway.

ID mapping and pathway assignment. Takes your list of IDs and finds the corresponding pathways from Reactome, plus the corresponding UniProt IDs. http://www.reactome.org/ReactomeGWT/entrypoint.html#PathwayAnalysisDataUploadPage

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