Protein Protein Interaction
3
2
Entering edit mode
12.9 years ago
Plasmid ▴ 160

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?

protein interaction database • 3.3k views
ADD COMMENT
3
Entering edit mode
ADD COMMENT
1
Entering edit mode
12.9 years ago
B. Arman Aksoy ★ 1.2k

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 COMMENT
1
Entering edit mode
12.9 years ago
Woa ★ 2.9k

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 COMMENT

Login before adding your answer.

Traffic: 2702 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6