Bioinformatics. 2008 Oct 15;24(20):2418-9. Epub 2008 Aug 20.

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

Persampieri J, Ritter DI, Lees D, Lehoczky J, Li Q, Guo S, Chuang JH.

Source

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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.

PMID:: 18718943; [PubMed - indexed for MEDLINE]
PMCID: PMC2562007

Free PMC Article

Images from this publication.See all images (1) Free text

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Substances

Grant Support

R21-HD051835/HD/NICHD NIH HHS/United States

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Libraries

LinkOut Holdings

Supplemental Content

Related citations

A systematic approach to identify functional motifs within vertebrate developmental enhancers. [Dev Biol. 2010]
A systematic approach to identify functional motifs within vertebrate developmental enhancers.
Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S. Dev Biol. 2010 Jan 15; 337(2):484-95. Epub 2009 Oct 20.
Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis. [Dev Biol. 2010]
Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis.
Kague E, Bessling SL, Lee J, Hu G, Passos-Bueno MR, Fisher S. Dev Biol. 2010 Jan 15; 337(2):496-505. Epub 2009 Nov 3.
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. [Genome Biol. 2007]
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.
Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G. Genome Biol. 2007; 8(2):R15.
Review Web-based tools and approaches to study long-range gene regulation in Metazoa. [Brief Funct Genomic Proteomic. 2009]
Review Web-based tools and approaches to study long-range gene regulation in Metazoa.
Fredman D, Engström PG, Lenhard B. Brief Funct Genomic Proteomic. 2009 Jul; 8(4):231-42. Epub 2009 Jul 15.
Review Organization of conserved elements near key developmental regulators in vertebrate genomes. [Adv Genet. 2008]
Review Organization of conserved elements near key developmental regulators in vertebrate genomes.
Woolfe A, Elgar G. Adv Genet. 2008; 61:307-38.

See reviews... See all...

Cited by 1 PubMed Central article

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. [Mol Biol Evol. 2010]
The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.
Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. Mol Biol Evol. 2010 Oct; 27(10):2322-32. Epub 2010 May 21.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

cneViewer: a database of conserved non-coding elements for studies of tissue-spe...
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation.
Bioinformatics. 2008 Oct 15 ;24(20):2418-9. Epub 2008 Aug 20 .

PubMed
The origins of apicomplexan sequence innovation.
The origins of apicomplexan sequence innovation.
Genome Res. 2009 Jul ;19(7):1202-13. Epub 2009 Apr 10 .

PubMed
Immortalization of human alveolar epithelial cells to investigate nanoparticle u...
Immortalization of human alveolar epithelial cells to investigate nanoparticle uptake.
Am J Respir Cell Mol Biol. 2008 Nov ;39(5):591-7. Epub 2008 Jun 6 .

PubMed
Enriched transcription factor binding sites in hypermethylated gene promoters in...
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells.
Bioinformatics. 2008 Aug 15 ;24(16):1745-8. Epub 2008 Jun 6 .

PubMed
Hypoglycaemia, liver necrosis and perinatal death in mice lacking all isoforms o...
Hypoglycaemia, liver necrosis and perinatal death in mice lacking all isoforms of phosphoinositide 3-kinase p85 alpha.
Nat Genet. 2000 Nov ;26(3):379-82.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: