Mammalian promoter database

The Mammalian Promoter Database (MPromDb) is a curated database of gene promoters identified from ChIP-seq.^[1] The proximal promoter region (upstream of the core-promoter region) contains the cis-regulatory elements of most of the transcription factors (TFs).^[2]

MPromDb

Content
Description	annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
Contact
Laboratory	Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
Authors	Ravi Gupta
Primary citation	Gupta & al. (2011)[1]
Release date	2010
Access
Website	http://bioinformatics.wistar.upenn.edu/MPromDb/

Recently, a better approach to annotate active promoters has been demonstrated with a combination of ChIP-seq and computational technique.^[3] This technique has been used to find the target genes of TFs in mammalian systems.^[4] The MPromDb is based on this technology. Curated promoter sequences for eukaryotic organisms are provided by an EPD database;^[5] however, promoter activity information at tissue/ cell centric level is not offered.

The MPromDb data base added active RNAP-II promoters identified after analyzing ten different mouse cell/tissue ChIP-seq experiments performed with RNAP-II antibodies and six different human cell types.^[1] The data was acquired by a series of computational methods followed by manual correction to ensure its high level quality.^[2] In the newest version of MPromDb, about 507 million uniquely-aligned RNA Pol-II ChIP-seq reads have already been analyzed from 26 different databases, including six human cell-types and 10 distinct mouse cell/tissues.^[1]