Drosophila DNase I Footprint Database (v2.0)
HomeSearchBrowse by TargetBrowse by Factor
 
Background
This page provides access to results of the systematic curation and genome annotation of 1,365 DNase I footprints for the fruitfly D. melanogaster reported in Bergman, Carlson and Celniker (2005) Bioinformatics 21:1747-1749. These data have been extracted from 201 primary references and provide a non-redundant set of high quality binding site information for 87 transcription factors and 101 target genes in one of the most important model systems. Unlike previous work, this dataset has been generated from a single experimental data type, represents all available developmental stages (including anterior-posterior, mesoderm and imaginal disk patterning), and is linked explicitly to finished genome sequence coordinates. This dataset should provide a useful resource for computational analyses of transcription factor binding site biology in the genus Drosophila.

Note! As of October 2007, the Drosophila DNAse I footprint database has fully merged with the REDfly database to provide a one-stop portal for cis-regulatory data in Drosophila. REDfly 2.0 aims to provide a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites in Drosophila that we hope will serve as a powerful resource for both computational and experimental studies of transcriptional regulation. The FlyReg website will remain as a static legacy resource, but will no loger be updated. For the most up-to-date cis-regulatory annotations and genome mappings in Drosophila, please visit at REDfly at http://redfly.ccr.buffalo.edu.
 
Search the Drosophila DNase I Footprint Database (v2.0)
Search by gene: A simple query interface to search for genes with binding site information in FlyReg 2.0 with links to FlyBase, PubMed and the UCSC genome browser showing alignments of footprints with D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, D. mojavensis, Anopheles gambiae and Apis mellifera.
 
Browse the Drosophila DNase I Footprint Database (v2.0)
Browse by Target: A hypertext document sorted by target gene with links to FlyBase, PubMed and the UCSC genome browser showing alignments of footprints with D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, D. mojavensis, Anopheles gambiae and Apis mellifera.

Browse by Factor: A hypertext document sorted by binding factor with links to FlyBase, PubMed and the UCSC genome browser showing alignments of footprints with D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, D. mojavensis, Anopheles gambiae and Apis mellifera.
 
Download the Drosophila DNase I Footprint Database (v2.0)
Download GFF: A text file in Sanger Institute's GFF v2 format with additional target, factor, PubMed ID fields. This file is an updated version on D. melanogaster Release 4 coordinates of Supplemental File 3 in Bergman, Carlson and Celniker (2005) Bioinformatics 21:1747-1749. Coordinates are UCSC's "half-open zero-based" system {e.g. a (start, end] pair of (100,200] represents bases 101-200 on the genome sequence}. The strand for genome sequence coordinates is purposefully not reported since a binding site is a double-stranded feature.

Download Sequences: A text file of sequences in FASTA format corresponding to footprinted regions on the plus strand of the D. melanogaster Release 4 genome sequence. A text file of file of sequences in FASTA format corresponding to footprinted regions extended by ±30 bp on the plus strand of the D. melanogaster Release 4 genome sequence can be found here.

Download SQL: A dump of the mySQL database (and documentation) used for data entry and storage derived from the GadFly schema.

NB: The GFF file (not the Sequences or mySQL dump) defines the information contained in v2.0.
 
Browse & Download the Literature (v2.0)
Browse PubMed (1984-1994) (1995-2004): Hypertext summaries of the 201 primary references that form the experimental foundation for this database.

Download XML: A tar.gz text file of 201 PubMed abstracts for literature mining.

An archive of the 131 primary references in .pdf format is available on request.
 
Release Log
Information about FlyReg releases can be found here.
FlyReg v1.0 can be found here.
FlyReg v1.1 can be found here.
 
Related Resources
  • FlyReg 2.0 has been incorporated into REDfly 2.0.
  • FlyReg 2.0 has been used to support Stein Aerts' cisTARGET genome-wide CRM predictions in Drosophila.
  • FlyReg 2.0 has been incorporated into the Drosophila cis-Regulatory Database.
  • FlyReg 2.0 has been used to support the Drosophila Transcription Factor Database.
  • FlyReg 2.0 has been incorporated into ORegAnno: The Open Regulatory Annotation Database.
  • FlyReg 2.0 has been incorporated into Ensembl. For an example of Ensembl's new GeneRegulationView click here.
  • FlyReg 2.0 has been incorporated into the public version of Transfac.
  • FlyReg 2.0 has been incorporated into the official annotation of the D. melanogaster genome.
  • The Drosophila DNase I footprint database has been included in the BioMedCentral Catalog of Databases on the web.
  • FlyReg v2.0 has been incorporated into FlyMine - an integrated database for genomic data in Drosophila and Anophleles.
  • FlyReg v2.0 has been incorporated as a track in the UCSC Drosophila melanogaster genome browser.

  • PWMs from Dan Pollard based on FlyReg 2.0 have been incorporated into the JASPAR database.
  • PWMs from Down et al. (2007) based on FlyReg 2.0 have been incorporated into the Drosophila melanogaster Major Position Matrix Motifs database.
  • 30 Position Weight Matrices (PWMs) from Down et al. (2007) derived from FlyReg 2.0 can be found here.
  • Dan Pollard (UC-Berkeley) has used MEME to generate made PWMs for many of the transcription factors in FlyReg. These PWMs are also available through Dmitri Papatsenko's ClusterDraw website.
  • Dmitri Papatsenko's group (UC-Berkeley) has curated binding site data for blastoderm transcription factors.
  • Michael Zhang's group (CSHL) has curated an independent set of binding site data at the Drosophila Binding Site Database.

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    Acknowledgements
    We thank Nicholas Blanchard for assistance with literature curation and FlyBase Cambridge for access to the Drosophila offprint collection. Angie Hinrichs and others helped with data import into the UCSC Genome Browser; Rachel Lyne and Kim Rutherford helped with data import into FlyMine; Andy Schroeder and others helped with the data import into FlyBase; Dmitri Chekmenev and others helped with the data import into Transfac; Thomas Down and others helped with the original data import into Ensembl; and Erin Pleasance and others helped with the data import into ORegAnno. We are grateful for the information, sequences, coordinates, and/or footprint data provided by Mariana Bienz, Olivier Cuvier, Kirsten Guss, Thomas Hader, Craig Hart, Michael Hoch, Herbert Jackle, Judith Lengyel, Guo-Jen Liao, Kevin Moses, Rolando Riviera-Pomar, Maria Saenz-Robles, Matthew Scott, William Stumph, Andrew Travers, Joseph Weiss, Cheng-Cai Zhang and Keji Zhao.
     
    Citation
    If you use this dataset in your research, please report the version number and cite Bergman, C.M., J.W Carlson and S.E. Celniker (2005) Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, D. melanogaster. Bioinformatics 21:1747-1749.

    If you intend to redistibute these data, please note the version number and provide a link to this page.
     
    Contact Information
    Email Casey Bergman (casey.bergman@manchester.ac.uk) with questions, comments or corrections.
     
    This page was last updated 11-Apr-2014