| MPromDb | |
| Description: | annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. |
| Laboratory: | Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA. |
| Author: | Ravi Gupta |
| Citation: | Gupta & al. (2011) |
| Released: | 2010 |
| Url: | http://bioinformatics.wistar.upenn.edu/MPromDb/ |
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]
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. 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]