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

Jason H Persampieri | Zendy; Deborah Ritter | Zendy; Daniel Lees | Zendy; Jessica A. Lehoczky | Zendy; Qiang Li | Zendy; Su Guo | Zendy; Jeffrey H. Chuang | Zendy

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

Author(s) -

Jason H Persampieri,

Deborah Ritter,

Daniel Lees,

Jessica A. Lehoczky,

Qiang Li,

Su Guo,

Jeffrey H. Chuang

Publication year - 2008

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btn443

Subject(s) - zebrafish , gene , computational biology , genome , coding (social sciences) , biology , conserved sequence , vertebrate , coding region , database , genetics , computer science , base sequence , statistics , mathematics

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.

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