Analyzing Open source PPI databases
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beingseema03 ▴ 10
@beingseema03-8707
Last seen 8.9 years ago
India

Hi all,
I want to analyze the databases of Protein Protein Interaction which are open source and freely available. I have
gone through the paper which is " An evaluation of human protein-protein interaction data in the public domain" by
Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi. They have analyzed different freely available datasets which are MINT , INTACT , HPRD , BIND, DIP , MIPS , PDZBase , and Reactome. The links of the available databases are mentioned in the paper but there is a list of databases available in it. They havent mentioned which kind of database they are using for analysis. Can any one provide a better source from where i can download This open source databases for analysis.
 

Thanks

ppi bioinformatics • 2.2k views
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Hi misovic,
Thanks for your response.But do you have any idea about the sources of databases which i mentioned..?? Because as a part of my project work i have to analyze these databases.

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@martin-morgan-1513
Last seen 3 months ago
United States

PSICQUIC federates several data bases; the Bioconductor package PSICQUIC accesses these.

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@martin will you please elaborate.. Is it giving access to those databases which i mentioned in my question..??
 

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Look at the link to the PSICQUIC project page, and you can see that some of the data bases you mention are listed there. Also look at the PSICQUIC package vignette for examples on how to use Bioconductor to access these data bases.

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@martin Thank you so much. Your answer helps me out from the problem i was facing from last few days.

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