Question

What Is The Best "Public" Resource For Protein-Dna Interactions?

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13.7 years ago

Keiichiro Ono ▴ 140

Hi. I'm a developer of biological network analysis/visualization software called Cytoscape. I'm planning to create a short tutorial for absolute beginners of biological network analysis. Currently I'm looking for a sample dataset which covers most common workflows.

There are tons of public PPI datasets, such as BioGRID, IntAct, STRING, etc. However, I do not know good, public database focused on Protein-DNA interactions. Does anyone know such public datasets? Since I'm going to use it in Cytoscape application, database with bulk download feature or web service access is preferable.

Thanks in advance. Kei

interaction pathway ppi visualization • 5.8k views

ADD COMMENT • link updated 13.7 years ago by Casey Bergman 18k • written 13.7 years ago by Keiichiro Ono ▴ 140

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Hi Keiichiro, welcome on Biostar

ADD REPLY • link 13.7 years ago by Pierre Lindenbaum 164k

score 6 · Answer 1 · 2011-04-02

I don't know which one is the 'best', but the following databases are in my lists:

hPDI: a database of experimental human protein-DNA interactions. http://www.ncbi.nlm.nih.gov/pubmed/19900953 download: http://bioinfo.wilmer.jhu.edu/PDI/download/download.html
BIPA: a database for protein-nucleic acid interaction in 3D structures http://www.ncbi.nlm.nih.gov/pubmed/19357098 download: http://mordred.bioc.cam.ac.uk/~semin/BIPA/
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. http://www.ncbi.nlm.nih.gov/pubmed/18842628 download http://thebrain.bwh.harvard.edu/uniprobe/downloads.php
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Ram · Answer 2 · 2011-04-02

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13.7 years ago

Magali Michaut ▴ 30

Hi Kei,

I don't know what is best and most appropriate for your need but here are a few more:

Cheers,
Magali

ADD COMMENT • link updated 5.3 years ago by Ram 44k • written 13.7 years ago by Magali Michaut ▴ 30

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welcome on Biostar Magali

ADD REPLY • link 13.7 years ago by Pierre Lindenbaum 164k

score 2 · Answer 3 · 2011-04-02

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13.7 years ago

Will 4.6k

Most (but not all) protein-DNA involve transcription factor based activation. TRANSFAC is probably the most well known database of protein to gene targets.

ADD COMMENT • link 13.7 years ago by Will 4.6k

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I think TRANSFAC is a good data source, but it's partially public. I'm a bit worried about its license. Thanks anyway.

ADD REPLY • link 13.7 years ago by Keiichiro Ono ▴ 140

score 2 · Answer 4 · 2011-04-02

I'm assuming if you want to visualize networks that you are looking for DBs that have data on protein-DNA interactions in the form of specific Transcription Factor -> Target Gene relations, rather than information about the overall DNA binding specificity of TFs (e.g. UniProbe, hDPI, Jaspar).

If so then ORegAnno and Pazar are probably your best bet for curated Transcription Factor -> Target Gene data. Both have APIs (ORegAnno and Pazar) and XML dumps. I think Pazar is a more active currently, and has the virtue of being a portal for many other datasets (including ORegAnno), so this may the better choice for your purposes.