Filtering only PPI from BioGRID

Question

[GD]

As stated in the subject: I am looking for a simple way to filter out only PPI interactions from the BioGRID interactions database.

How could I do it?

Answer 1

[Jean-Karim Heriche]

In the BioGRID tab-delimited file, column 7 is called 'EXPERIMENTAL_SYSTEM' and describes how the interaction was obtained e.g. two-hybrid. You could use this to filter for the types of interaction you're interested in. You can find a list of terms here.

[GD]

*edit: new post opened here, :) . Feel free to answer there, if you like.

Thank you for the hint!

I downloaded the current BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c-3.4.132.mitab and, I see that:

1. there are other methods to detect PPIs, such as: FRET, PCA, Co-fractionation, Co-purification [...];
2. there are entries with no confidence-score provided ("-" at column 15) .

My question is:

Given (2), what methods have been proved to be, among the others, more reliable in detecting PPIs?

Maybe this question is better suited for a separate post.

Answer 2

[GD]

Which EXPERIMENTAL_SYSTEMs should I filter, in order to get only protein-protein physical direct interactions?

Sorry, I am not a lab-guy. :)

*edit

I clarify what my goal is.

I'd like to extract only interactions (interactor A, interactor B) such that , for both of them, I can extract the corresponding FASTA sequences.

[Jean-Karim Heriche]

The listed methods typically considered to show direct interactions are: two-hybrid, reconstituted complex, protein-peptide, PCA, FRET, far Western and biochemical activity. I normally would consider co-crystal structure as indicative of direct interaction, except that here they also include NMR and EM structures which may not have the resolution to resolve direct interactions.
For any interaction, you can retrieve protein sequences using the IDs provided. However, the tab-delimited files only give gene IDs of interacting partners. For protein IDs, you'll need to get the PSI-MI 2.5 files.