Question: Cytoscape Plug-In For Retrieving Protein-Protein Interactions
2
gravatar for Woa
6.1 years ago by
Woa2.6k
United States
Woa2.6k wrote:

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

ppi cytoscape • 4.5k views
ADD COMMENTlink written 6.1 years ago by Woa2.6k
2
gravatar for pixie@bioinfo
6.1 years ago by
pixie@bioinfo1.1k
India
pixie@bioinfo1.1k wrote:

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/

ADD COMMENTlink written 6.1 years ago by pixie@bioinfo1.1k

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

ADD REPLYlink written 6.1 years ago by Woa2.6k
1
gravatar for Arnaud Ceol
6.1 years ago by
Arnaud Ceol750
Milan, Italy
Arnaud Ceol750 wrote:

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.

ADD COMMENTlink written 6.1 years ago by Arnaud Ceol750

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

ADD REPLYlink written 6.1 years ago by Woa2.6k
0
gravatar for Patrik
6.0 years ago by
Patrik0
Patrik0 wrote:

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

ADD COMMENTlink written 6.0 years ago by Patrik0
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