Question: What'S The Most Comprehensive Database/Resource For Human Protein-Protein Interactions?
1
gravatar for enricoferrero
6.6 years ago by
enricoferrero780
United Kingdom
enricoferrero780 wrote:

I need to programmatically access human protein-protein interactions to retrieve interactions between specific classes of molecules, but there are many protein-protein interactions databases around, especially for Homo sapiens (e.g. BIOGrid, HPRD, Reactome, MINT, DIP, STRING... just to name a few).

What's the most comprehensive resource altogether? Is there a database that somehow integrates all of the other ones? I'd just need a flat text file with all the interactions and the classes of the interacting molecules (e.g. 'transcription factor', 'GTPase', 'lipid phosphatase'...).

Thanks!

interaction database human • 3.3k views
ADD COMMENTlink modified 6.6 years ago by Diwan560 • written 6.6 years ago by enricoferrero780
1

David has suggested a R code for my question earlier. It might be useful. Check this link: http://brainchronicle.blogspot.co.uk/2012/05/obtain-protein-protein-interaction-from.html

ADD REPLYlink written 6.6 years ago by Diwan560
5
gravatar for Noa
6.6 years ago by
Noa50
Noa50 wrote:

Yes the HIPPIE database (Scheafer et al 2012) combines all human PPI data from 11 databses and manually curated papers

ADD COMMENTlink written 6.6 years ago by Noa50

This is a good suggestion - It looks to me like HIPPIE provides more human interactions thatn Bisogenet, and the database can easily be downloaded.

http://cbdm.mdc-berlin.de/tools/hippie/download.php

I will probably use this resource in the future!

ADD REPLYlink written 6.6 years ago by Charles Warden7.5k
2
gravatar for Heather Vincent
6.6 years ago by
Manchester, UK
Heather Vincent160 wrote:

For open-source resources try PSIQUIC View (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml). Set the organism field to 'human'.

ADD COMMENTlink written 6.6 years ago by Heather Vincent160
1
gravatar for Charles Warden
6.6 years ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

If your institution has a license, IPA should contain information from most of all of these databases. This is what I would use.

MetaGO is another commercial program that I know of with similar functionality that could probably also accomplish this.

For an open-source solution, I would check out the files provided by NCBI. For example, if you search any gene (like BRCA1) in NCBI Gene, you can find all of this information. Therefore, I assume the information can be obtained somehow from the NCBI flat files:

Example: http://www.ncbi.nlm.nih.gov/gene/672

NCBI FTP: http://www.ncbi.nlm.nih.gov/Ftp/

ADD COMMENTlink written 6.6 years ago by Charles Warden7.5k
1
gravatar for Diwan
6.6 years ago by
Diwan560
United States
Diwan560 wrote:

I found Bisogenet cytoscape plugin very helpful. It uses sysbiomics database that includes most of the above.

link: http://bio.cigb.edu.cu/SBweb/index.jsp

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Diwan560
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