Mammalian promoter database

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)[1]
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.[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]

References

  1. ^ a b c d 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. ^ a b 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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