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Mammalian promoter database

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MPromDb
Content
Descriptionannotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
Contact
LaboratoryCenter for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
AuthorsRavi Gupta
Primary citationGupta & al. (2011)
Release date2010
Access
Websitehttp://bioinformatics.wistar.upenn.edu/MPromDb/

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

Recently, a better approach to annotate active promoters has been demonstrated with a combination of ChIP-seq and computational technique. This technique has been used to find the target genes of TFs in mammalian systems. The MPromDb is based on this technology. Curated promoter sequences for eukaryotic organisms are provided by an EPD database; 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. 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.

References

  1. ^ Gupta, Ravi; Bhattacharyya Anirban; Agosto-Perez Francisco J; Wickramasinghe Priyankara; Davuluri Ramana V (Jan 2011). "MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data". Nucleic Acids Res. 39 (Database issue). England: D92-7. doi:10.1093/nar/gkq1171. PMC 3013732. PMID 21097880.
  2. ^ Sun, Hao; Palaniswamy, Saranyan K.; Pohar, Twyla T. (2006). "MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data". Nucleic Acids Research. 34 (Database issue): 98–103. doi:10.1093/nar/gkj096. PMC 1347458. PMID 16381984.
  3. Sun, H; Wu, J; Wickramasinghe, P; Pal, S; Gupta, R; Bhattacharyya, A; Agosto-Perez, FJ; Showe, LC; Huang, TH; Davuluri, RV (Jan 2011). "Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq". Nucleic Acids Res. 39 (1): 190–201. doi:10.1093/nar/gkq775. PMC 3017616. PMID 20843783.
  4. Weinmann, A.S.; Yan, P.S.; Oberley, M.J.; Huang, T.H.; Farnham, P.J. (2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation". Genes Dev. 16 (2): 235–244. doi:10.1101/gad.943102. PMC 155318. PMID 11799066.
  5. Schmid, C.D.; Perier, R.; Praz, V.; Bucher, P. (2006). "EPD in its twentieth year: towards complete promoter coverage of selected model organisms". Nucleic Acids Res. 34 (Database issue): 82–85. doi:10.1093/nar/gkj146. PMC 1347508. PMID 16381980.

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