Genome-wide promoter extraction and analysis in hu...[Genome Biol. 2005]

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1: Genome Biol. 2005;6(8):R72. Epub 2005 Aug 1. Links

Genome-wide promoter extraction and analysis in human, mouse, and rat.

Xuan Z, Zhao F, Wang J, Chen G, Zhang MQ.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. xuan@cshl.edu

Large-scale and high-throughput genomics research needs reliable and comprehensive genome-wide promoter annotation resources. We have conducted a systematic investigation on how to improve mammalian promoter prediction by incorporating both transcript and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence to create CSHLmpd (Cold Spring Harbor Laboratory Mammalian Promoter Database) for the biomedical research community, which can act as a starting reference system for more refined functional annotations.

PMID: 16086854 [PubMed - indexed for MEDLINE]

PMCID: PMC1273639

HumanUpstream and MouseUpstream: databases of promoter sequences in the human and mouse genomes. [OMICS. 2005]
angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences. [BMC Genomics. 2006]
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. [Nucleic Acids Res. 2006]
ReviewCurrent bioinformatics tools in genomic biomedical research (Review). [Int J Mol Med. 2006]
ReviewPerformance assessment of promoter predictions on ENCODE regions in the EGASP experiment. [Genome Biol. 2006]

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Genome-wide promoter extraction and analysis in human, mouse, and rat.

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