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MPromDb specifications

Information


Unique identifier OMICS_01876
Name MPromDb
Alternative name Mammalian Promoter Database
Restrictions to use None
Version 2.1
Maintained No
Wikipedia https://en.wikipedia.org/wiki/Mammalian_promoter_database

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publications for Mammalian Promoter Database

MPromDb citations

 (11)
library_books

The handedness associated PCSK6 locus spans an intronic promoter regulating novel transcripts

2016
Hum Mol Genet
PMCID: 4986331
PMID: 26908617
DOI: 10.1093/hmg/ddw047

[…] region were queried for allelic effects on protein–DNA binding affinity using the TRANSFAC () and Genomatix MatInspector () databases. Promoter predictions were conducted with PROSCAN v1.7 () and the Mammalian Promoter Database (MPromDb) (). Protein domain predictions were conducted with Interpro (). […]

library_books

Genome scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia

2015
Leukemia
PMCID: 4705427
PMID: 26126967
DOI: 10.1038/leu.2015.172

[…] n of ChIP-Seq and gene expression data. All analysis was performed in R with plots created using ggplot2.Peaks were assigned to genes using annotation from UCSC. Peaks within regions contained in the mammalian promoter database MPromdDb were allocated to promoter or within the gene body to intragenic. The remaining intergenic peaks were assigned to both the nearest 5' and 3' genes. If no gene was […]

library_books

A Provisional Gene Regulatory Atlas for Mouse Heart Development

2014
PLoS One
PMCID: 3885437
PMID: 24421884
DOI: 10.1371/journal.pone.0083364

[…] MPromDb (Mammalian Promoter Database) is a curated database that annotates gene promoters identified with ChIP-seq which is one of the most robust approaches of defining gene promoters . The ChIP-seq […]

library_books

Chromatin Changes in Dicer Deficient Mouse Embryonic Stem Cells in Response to Retinoic Acid Induced Differentiation

2013
PLoS One
PMCID: 3767645
PMID: 24040281
DOI: 10.1371/journal.pone.0074556

[…] possible to avoid background resulting from genomic contamination of RNA samples. Primers for ChIP-qPCR were designed to span promoter regions of the assayed genes derived from the Cold Spring Harbor mammalian promoter database (http://rulai.cshl.edu/CSHLmpd2/). The complete lists of primers used for ChIP-qPCR assays are listed in . […]

library_books

Application of an Integrative Computational Framework in Trancriptomic Data of Atherosclerotic Mice Suggests Numerous Molecular Players

2012
Adv Bioinformatics
PMCID: 3502768
PMID: 23193398
DOI: 10.1155/2012/453513

[…] e method: Average, distance: Cosine) in Gene ARMADA. Promoter sequences from −700 to +300, relative to transcription start site, were downloaded for mouse and human from Cold Spring Harbor Laboratory Mammalian Promoter Database (CSHLmpd) []. In the cases that alternative promoters were given for the same gene, we selected the one defined as the “best" at []. For promoters that we could not detect […]

library_books

Triplex DNA binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

2012
Mol Cancer
PMCID: 3537547
PMID: 22682314
DOI: 10.1186/1476-4598-11-38

[…] ites in the U2AF65 (U2AF2) gene promoter did not indicate any beta-catenin or TCF family transcription factor sites among the 55 high-scoring (>85%) sites we identified (Cold Spring Harbor Laboratory Mammalian Promoter Database http://rulai.cshl.edu/CSHLmpd2/; Transcription Factor Search http://www.cbrc.jp/research/db/TFSEARCH.html). Similarly, mining through microarray expression studies revealed […]

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MPromDb institution(s)
Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio Stage University, Columbus, OH, USA

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