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Nucleic Acids Research 2005 33(Database Issue):D91-D97; doi:10.1093/nar/gki103
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Nucleic Acids Research, 2005, Vol. 33, Database issue D91-D97
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites

Voichita D. Marinescu, Isaac S. Kohane and Alberto Riva*

Children's Hospital Informatics Program, Children's Hospital Boston, Harvard Medical School, Enders Research Building EN-150.9, 300 Longwood Avenue, Boston, MA 02115, USA

* To whom correspondence should be addressed. Tel: +1 617 355 2178; Fax: +1 617 730 0921; Email: Alberto.Riva{at}tch.harvard.edu

Received August 15, 2004; Revised October 6, 2004; Accepted October 14, 2004

We describe a comprehensive map of putative transcription factor binding sites (TFBSs) across multiple genomes created using a search method that relies on hidden Markov models built from experimentally determined TFBSs. Using the information in the TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to scan regions 10 kb upstream of the start of the transcript for all known genes in the human, mouse and Drosophila melanogaster genomes. The results, together with homology information on clusters of ortholog genes across the three genomes, were used to create a multi-organism catalog of annotated TFBSs. The catalog can be queried through a web interface accessible at http://bio.chip.org/mapper that allows the identification, visualization and selection of TFBSs occurring in the promoter of a gene of interest and also the common factors predicted to bind across the cluster of orthologs that includes that gene. Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes.

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