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?
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
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.
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
