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Bioinformatics Advance Access published online on November 30, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti173
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 5, 2004
Revised November 5, 2004
Accepted November 20, 2004

Applications note

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, D. melanogaster

Casey M. Bergman 1*, Joseph W. Carlson 2, and Susan E. Celniker 2

1 Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
2 Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

* To whom correspondence should be addressed.
Casey M. Bergman, E-mail: cbergman{at}gen.cam.ac.uk


  Abstract

Summary: Despite increasing numbers of computational tools developed to predict cis-regulatory sequences, the availability of high-quality data sets of transcription factor binding sites limits advances in the bioinformatics of gene regulation. Here we present such a dataset based on a systematic literature curation and genome annotation of DNase I footprints for the fruitfly, Drosophila melanogaster. Using the experimental results of 201 primary references, we annotated 1,367 binding sites from 87 transcription factors and 101 target genes in the D. melanogaster genome sequence. These data will provide a rich resource for future bioinformatics analyses of transcriptional regulation in Drosophila such as constructing motif models, training cis-regulatory module detectors, benchmarking alignment tools and continued text mining of the extensive literature on transcriptional regulation in this important model organism.

Availability: http://www.flyreg.org/.


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