MPromDb

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

Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X Jin, Hui-ming Huang, Ramana V. Davuluri

Research output: Contribution to journalArticle

32 Citations (Scopus)

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.

Original languageEnglish (US)
JournalNucleic acids research.
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006
Externally publishedYes

Fingerprint

Databases
Genes
CpG Islands
Chromatin Immunoprecipitation
Transcription Initiation Site
Nucleic Acid Databases
Computational Biology
PubMed
Exons
Transcription Factors
Binding Sites
Genome

ASJC Scopus subject areas

  • Genetics

Cite this

MPromDb : an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. / Sun, Hao; Palaniswamy, Saranyan K.; Pohar, Twyla T.; Jin, Victor X; Huang, Hui-ming; Davuluri, Ramana V.

In: Nucleic acids research., Vol. 34, No. Database issue, 01.01.2006.

Research output: Contribution to journalArticle

@article{92f0b6c3d79440ca84c9ff0803158d51,
title = "MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.",
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.",
author = "Hao Sun and Palaniswamy, {Saranyan K.} and Pohar, {Twyla T.} and Jin, {Victor X} and Hui-ming Huang and Davuluri, {Ramana V.}",
year = "2006",
month = "1",
day = "1",
language = "English (US)",
volume = "34",
journal = "Nucleic acids research.",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "Database issue",

}

TY - JOUR

T1 - MPromDb

T2 - an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

AU - Sun, Hao

AU - Palaniswamy, Saranyan K.

AU - Pohar, Twyla T.

AU - Jin, Victor X

AU - Huang, Hui-ming

AU - Davuluri, Ramana V.

PY - 2006/1/1

Y1 - 2006/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33644878173&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33644878173&partnerID=8YFLogxK

M3 - Article

VL - 34

JO - Nucleic acids research.

JF - Nucleic acids research.

SN - 0305-1048

IS - Database issue

ER -