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CONDOR: a database resource of developmentally associated conserved non-coding elements

Adam Woolfe12, Debbie K Goode1, Julie Cooke1, Heather Callaway1, Sarah Smith1, Phil Snell1, Gayle K McEwen12 and Greg Elgar1*

Author Affiliations

1 School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK

2 Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20870, USA

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BMC Developmental Biology 2007, 7:100  doi:10.1186/1471-213X-7-100

Published: 30 August 2007

Abstract

Background

Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal cis-regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them.

Description

Here we present CONDOR (COnserved Non-coDing Orthologous Regions) available at: http://condor.fugu.biology.qmul.ac.uk webcite. In an interactive and intuitive way the website displays data on > 6800 non-coding elements associated with over 120 early developmental genes and conserved across vertebrates. The database regularly incorporates results of ongoing in vivo zebrafish enhancer assays of the CNEs carried out in-house, which currently number ~100. Included and highlighted within this set are elements derived from duplication events both at the origin of vertebrates and more recently in the teleost lineage, thus providing valuable data for studying the divergence of regulatory roles between paralogs. CONDOR therefore provides a number of tools and facilities to allow scientists to progress in their own studies on the function and evolution of developmental cis-regulation.

Conclusion

By providing access to data with an approachable graphics interface, the CONDOR database presents a rich resource for further studies into the regulation and evolution of genes involved in early development.