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Database Commons - MPromDb

MPromDb

Citations: 79

z-index 0.00

Short name MPromDb
Full name Mammalian Promoter Database
Description MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results.The long term goal of this database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics.
URL http://mpromdb.wistar.upenn.edu/
Year founded 2005
Last update & version 9/15/2010    v2.1
Availability Free to all users
University/Institution hosted The Wistar Institute
Address Philadelphia,PA,USA
City Philadelphia
Province/State PA
Country/Region United States
Contact name Ramana V. Davuluri
Contact email rdavuluri@wistar.org
Data type(s)
Major organism(s)
Keyword(s)
  • ChIP-seq
  • gene promoter
Publication(s)
  • MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. [PMID: 21097880]

    Ravi Gupta, Anirban Bhattacharyya, Francisco J Agosto-Perez, Priyankara Wickramasinghe, Ramana V Davuluri
    Nucleic acids research 2011:39(Database issue)
    31 Citations (Google Scholar as of 2016-02-27)

    Abstract: MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 different data sets that include six human cell-types and 10 distinct mouse cell/tissues. The updated MPromDb version consists of computationally predicted (novel) and known active RNAP-II promoters (42,893 human and 48,366 mouse promoters) from various data sets freely available at NCBI GEO database. We found that 36% and 40% of protein-coding genes have alternative promoters in human and mouse genomes and ?40% of promoters are tissue/cell specific. The identified RNAP-II promoters were annotated using various known and novel gene models. Additionally, for novel promoters we looked into other evidences-GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA-seq reads. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. We have also integrated GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations. The current release of MPromDb can be accessed at http://bioinformatics.wistar.upenn.edu/MPromDb/.

  • MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. [PMID: 16381984]

    Hao Sun, Saranyan K Palaniswamy, Twyla T Pohar, Victor X Jin, Tim H-M Huang, Ramana V Davuluri
    Nucleic acids research 2006:34(Database issue)
    48 Citations (Google Scholar as of 2016-02-16)

    Abstract: We have developed Mammalian Promoter Database (MPromDb), a novel database that integrates gene promoters with experimentally supported annotation of transcription start sites, cis-regulatory elements, CpG islands and chromatin immunoprecipitation microarray (ChIP-chip) experimental results with intuitively designed presentation. Release 1.0 of MPromDb currently contains 36,407 promoters and first exons (19,170 from human, 15,953 from mouse and 1284 from rat), 3739 transcription factor (TF)-binding sites (2027 from human, 1181 mouse and 531 rat) and 224 TFs with links to PubMed and GenBank references. Target promoters of TFs that have been identified by ChIP-chip assay are integrated into the database. MPromDb serves as a portal for genome-wide promoter analysis of data generated by ChIP-chip experimental studies. MPromDb can be accessed from http://bioinformatics.med.ohio-state.edu/MPromDb.

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Tags

DNA Expression
Mammal
ChIP-seq gene promoter

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-26]
    • Li Yang [2015-06-26]
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