Is there a level (distance) criteria about protein relationship in the PPI network?

Question

[carlos_marchi]

For example, is there a PPI network where protein P1 is related to P2, P2 with P3. Can I suppose that P1 related to P3 because the relationship between P2 and P3?

Is there a criteria about the relationship level between two proteins? In this case, I will use shortest path algorithm to get the distance of proteins.

Thank you very much.

Answer 1

[lieven.sterck]

no expert on PPI networks but there is a high risk of assuming things that are not there (or true).

It is definitely so that P1 can interact with P2 and P2 with P3, but there is no chance (or indication) that P1 can (directly!!!) interact with P3 . (they can for instance bind/target different regions in P2) , transitive reasoning here might be dangerous.

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