![]() | This article may be too technical for most readers to understand.(September 2018) |
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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/ |
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. [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]
![]() | This article may be too technical for most readers to understand.(September 2018) |
![]() | |
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/ |
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. [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]