Question: Analyzing Open source PPI databases
1
gravatar for beingseema03
4.1 years ago by
beingseema0310
India
beingseema0310 wrote:

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

bioinformatics ppi • 834 views
ADD COMMENTlink modified 4.1 years ago by Martin Morgan ♦♦ 23k • written 4.1 years ago by beingseema0310
Answer: Analyzing Open source PPI databases
1
gravatar for branislav misovic
4.1 years ago by
Netherlands/Amsterdam
branislav misovic120 wrote:

hi,
I would check :

http://www.bioconductor.org/packages/devel/bioc/html/RpsiXML.html
has 8 DBs

 and  STRING:
http://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html


...  but   also browse   bioC views:
http://www.bioconductor.org/packages/release/BiocViews.html#___GraphAndNetwork
http://www.bioconductor.org/packages/release/BiocViews.html#___Network
http://www.bioconductor.org/packages/release/BiocViews.html#___NetworkInference
http://www.bioconductor.org/packages/release/BiocViews.html#___Proteomics

 

ADD COMMENTlink written 4.1 years ago by branislav misovic120

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.

ADD REPLYlink written 4.1 years ago by beingseema0310
Answer: Analyzing Open source PPI databases
1
gravatar for Martin Morgan
4.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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

ADD COMMENTlink written 4.1 years ago by Martin Morgan ♦♦ 23k

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

ADD REPLYlink written 4.1 years ago by beingseema0310

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.

ADD REPLYlink written 4.1 years ago by Martin Morgan ♦♦ 23k

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

ADD REPLYlink written 4.1 years ago by beingseema0310
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