Journal Article

cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation

Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo and Jeffrey H. Chuang

in Bioinformatics

Volume 24, issue 20, pages 2418-2419
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn443
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation

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Summary: There are thousands of strongly conserved non-coding elements (CNEs) in vertebrate genomes, and their functions remain largely unknown. However, without biologically relevant criteria for prioritizing them, selecting a particular CNE sequences to study can be haphazard. To address this problem, we present cneViewer—a database and webtool that systematizes information on conserved non-coding DNA elements in zebrafish. A key feature here is the ability to search for CNEs that may be relevant to tissue-specific gene regulation, based on known developmental expression patterns of nearby genes. cneViewer provides this and other organizing features that significantly facilitate experimental design and CNE analysis.

Availability: http://cneviewer.zebrafishcne.org

Contact: chuangj@bc.edu

Journal Article.  1126 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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