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PMID: 16381984 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Nucleic acids research ·Vol. 34 ·No. Database issue ·2006-01-01 ·Pages D98-103

Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV

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.

MeSH Terms
Animals Binding Sites Chromatin Immunoprecipitation Computational Biology Computer Graphics Databases, Nucleic Acid Exons Genomics Humans Internet Mice Oligonucleotide Array Sequence Analysis Promoter Regions, Genetic Rats Systems Integration Transcription Factors/metabolism Transcription Initiation Site User-Computer Interface
Chemicals
Transcription Factors
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Sun Hao
Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio Stage University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA.
Palaniswamy Saranyan K
Pohar Twyla T
Jin Victor X
Huang Tim H-M
Davuluri Ramana V
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkj096
Published
2006-01-01
Pages
D98-103
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1347458
Subset
IM
Grants
NCI NIH HHS · P50 CA-11300 · United States
External Links
PubMed source DOI: 10.1093/nar/gkj096 PMC Full Text View journal details
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