Cytoscape Plug-In For Retrieving Protein-Protein Interactions

Question

[Woa]

I wish to find out all interactions WITHIN a set of around 200 HUMAN proteins. The identifiers I can use are genename, Uniprotaccession and Uniprot_Ids. So far I tried two plugins viz. MIMI and APID2NET.

MIMI doesn't seem to accept 200 proteins in one go, so I've to merge the networks. APID2NET shows too many nodes without any interactions. The STRING DB shows quite a many interactions for which MIMI/APID2NET don't report anything.

I tried the STRING plugin too, but it looks like it can accept one ID at a time. Am I missing something here?

Can somebody recommend some good and hassle less plugins/tricks to import PPIs. I've to do subsequently a BINGO analysis.

Thanks in advance

WoA

Answer 1

[pixie@bioinfo]

You can look into BisoGenet plugin and it imports data from DIP, BIOGRID, HPRD, BIND, MINT and INTACT.

It also gives the GO, KEGG pathway information for each gene in the network. For each of the edges, it gives the database entry, the type of experiment and the corresponding PMIDs.

Link: http://bio.cigb.edu.cu/bisogenet-cytoscape/

[Woa]

Many Thanks !!!. This serves well my purpose.

Answer 2

[Arnaud Ceol]

You may have a look at the Psicquic plugin : http://code.google.com/p/psicquic/wiki/CytoscapeClient

I didn't tried it myself but you should be able to query a list of protein and to search simultaneously all the psicquic provider databases.

[Woa]

Thanks for Psicquic. I however was not able to figure out if it can optionally find interactions only WITHIN a given set of proteins.

Answer 3

[Patrik]

BiosGenEt only works with some organisms, not all available in Intact for example