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

TitlecneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation.
Publication TypeJournal Article
Year of Publication2008
AuthorsPersampieri, J, Ritter, DI, Lees, D, Lehoczky, J, Li, Q, Guo, S, Chuang, JH
JournalBioinformatics
Volume24
Issue20
Pagination2418-9
Date Published2008 Oct 15
ISSN1367-4811
KeywordsAnimals, Base Sequence, Computational Biology, Conserved Sequence, Databases, Genetic, DNA, Gene Expression Regulation, Humans, Internet, Molecular Sequence Data, Regulatory Sequences, Nucleic Acid, Software, Zebrafish
Abstract

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.

DOI10.1093/bioinformatics/btn443
Alternate JournalBioinformatics
PubMed ID18718943
PubMed Central IDPMC2562007
Grant ListR21-HD051835 / HD / NICHD NIH HHS / United States