Question: Protein Protein Interaction
2
gravatar for Plasmid
7.9 years ago by
Plasmid160
European Union
Plasmid160 wrote:

I am new in protein interaction. I downloaded a interaction file of a protein from BioGrid database. I put this file into Cytoscape to view the interaction. In this case I only observed interaction with central protein. Is there anyway that I can get also interaction among the proteins and interaction with central protein? Are there other database that give me the same result?

interaction protein database • 1.9k views
ADD COMMENTlink written 7.9 years ago by Plasmid160
3
gravatar for Pierre Lindenbaum
7.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

The STRING Api returns all the interactions between the proteins.

eg. with eif4G1:

as XML:

http://string-db.org/api/psi-mi/interactionsList?identifiers=9606.ENSP00000316879

or as TSV:

http://string-db.org/api/psi-mi-tab/interactionsList?identifiers=9606.ENSP00000316879

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 7.9 years ago by Pierre Lindenbaum124k
1
gravatar for B. Arman Aksoy
7.9 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

You can also download tab-limited dump file for HPRD directly from their website, http://www.hprd.org/download, or you can go with the Pathway Commons normalized SIF exports of various other data sources: http://www.pathwaycommons.org/pc-snapshot/current-release/sif/by_source/

These are huge 'interactome's though; Cytoscape will only build the network in the background but for visualization, you probably have to right click on the network (from the left-side menu) and use the 'create view' option explicitly.

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 7.9 years ago by B. Arman Aksoy1.2k
1
gravatar for Woa
7.9 years ago by
Woa2.7k
United States
Woa2.7k wrote:

There are some Plugins available for Cytoscape that can add interactions within the selected nodes viz. MIMI, APID2NET and BISOGENET

Cytoscape Plug-In For Retrieving Protein-Protein Interactions

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 7.9 years ago by Woa2.7k
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