Biointelligence

January 13, 2010

Database of human Protein-DNA Interactions – hPDI

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 6:05 am
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The characterization of the protein-DNA interactions usually requires three levels of analysis:

1.Genetic: Determination of the nucleotide sequence of the protein-binding region and the identification of sequence changes that confer a mutated phenotype.

2. Biochemical: Identification of potential protein-DNA contacts using a variety of footprinting and protection experiments such as DNaseI or hydroxyl radical footprinting, and methylation protection or ethylation protection experiments.

3. Physical: Analysis of specific interactions in protein-target sequence fragment co-crystals.

The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The current release of hPDI contains 17,718 protein-DNA interactions for 1013 human DNA-binding proteins. These DNA-binding proteins include 493 human transcription factors (TFs) and 520 unconventional DNA binding proteins (uDBPs). This database is freely accessible for any academic purposes.

hPDI can be accessed from here: http://www.xiezhi.org/hpdi-database