What Is The Best "Public" Resource For Protein-Dna Interactions?
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10.7 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 • 4.9k views
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Hi Keiichiro, welcome on Biostar

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10.7 years ago

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

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10.7 years ago

Hi Kei,

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

Cheers,
Magali

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welcome on Biostar Magali

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10.7 years ago
Will 4.5k

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

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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.

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10.7 years ago

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.

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