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Literature DB >> 18718943

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

Jason Persampieri¹, Deborah I Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, Jeffrey H Chuang.

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.

Entities: Species

Mesh：

Substances：
DNA

Year: 2008 PMID： 18718943 PMCID： PMC2562007 DOI： 10.1093/bioinformatics/btn443

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

7 in total

1. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Authors: Ivan Ovcharenko; Marcelo A Nobrega; Gabriela G Loots; Lisa Stubbs
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

Review 2. Enhancer identification through comparative genomics.

Authors: Axel Visel; James Bristow; Len A Pennacchio
Journal: Semin Cell Dev Biol Date: 2007-01-05 Impact factor: 7.727

3. The Zebrafish Information Network: the zebrafish model organism database.

Authors: Judy Sprague; Leyla Bayraktaroglu; Dave Clements; Tom Conlin; David Fashena; Ken Frazer; Melissa Haendel; Douglas G Howe; Prita Mani; Sridhar Ramachandran; Kevin Schaper; Erik Segerdell; Peiran Song; Brock Sprunger; Sierra Taylor; Ceri E Van Slyke; Monte Westerfield
Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971

4. VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Authors: Axel Visel; Simon Minovitsky; Inna Dubchak; Len A Pennacchio
Journal: Nucleic Acids Res Date: 2006-11-27 Impact factor: 16.971

5. Highly conserved non-coding sequences are associated with vertebrate development.

Authors: Adam Woolfe; Martin Goodson; Debbie K Goode; Phil Snell; Gayle K McEwen; Tanya Vavouri; Sarah F Smith; Phil North; Heather Callaway; Krys Kelly; Klaudia Walter; Irina Abnizova; Walter Gilks; Yvonne J K Edwards; Julie E Cooke; Greg Elgar
Journal: PLoS Biol Date: 2004-11-11 Impact factor: 8.029

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

Authors: Adam Woolfe; Debbie K Goode; Julie Cooke; Heather Callaway; Sarah Smith; Phil Snell; Gayle K McEwen; Greg Elgar
Journal: BMC Dev Biol Date: 2007-08-30 Impact factor: 1.978

7. Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes.

Authors: Pär G Engström; David Fredman; Boris Lenhard
Journal: Genome Biol Date: 2008-02-15 Impact factor: 13.583

7 in total

13 in total

1. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Authors: Deborah I Ritter; Qiang Li; Dennis Kostka; Katherine S Pollard; Su Guo; Jeffrey H Chuang
Journal: Mol Biol Evol Date: 2010-05-21 Impact factor: 16.240

2. A systematic approach to identify functional motifs within vertebrate developmental enhancers.

Authors: Qiang Li; Deborah Ritter; Nan Yang; Zhiqiang Dong; Hao Li; Jeffrey H Chuang; Su Guo
Journal: Dev Biol Date: 2009-10-20 Impact factor: 3.582

3. Identification and characterization of new long conserved noncoding sequences in vertebrates.

Authors: Yoshiyuki Sakuraba; Toru Kimura; Hiroshi Masuya; Hideki Noguchi; Hideki Sezutsu; K Ryo Takahasi; Atsushi Toyoda; Ryutaro Fukumura; Takuya Murata; Yoshiyuki Sakaki; Masayuki Yamamura; Shigeharu Wakana; Tetsuo Noda; Toshihiko Shiroishi; Yoichi Gondo
Journal: Mamm Genome Date: 2008-11-18 Impact factor: 2.957

4. The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.

Authors: Aaron M Wenger; Shoa L Clarke; James H Notwell; Tisha Chung; Geetu Tuteja; Harendra Guturu; Bruce T Schaar; Gill Bejerano
Journal: PLoS Genet Date: 2013-08-29 Impact factor: 5.917

5. UCbase 2.0: ultraconserved sequences database (2014 update).

Authors: Vincenzo Lomonaco; Riccardo Martoglia; Federica Mandreoli; Laura Anderlucci; Warren Emmett; Silvio Bicciato; Cristian Taccioli
Journal: Database (Oxford) Date: 2014-06-19 Impact factor: 3.451

Review 6. Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective.

Authors: Manas Joshi; Adamandia Kapopoulou; Stefan Laurent
Journal: Front Genet Date: 2021-07-02 Impact factor: 4.599

7. Hundreds of conserved non-coding genomic regions are independently lost in mammals.

Authors: Michael Hiller; Bruce T Schaar; Gill Bejerano
Journal: Nucleic Acids Res Date: 2012-10-05 Impact factor: 16.971

8. UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.

Authors: Slavica Dimitrieva; Philipp Bucher
Journal: Nucleic Acids Res Date: 2012-11-27 Impact factor: 16.971

9. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

Authors: Michael Hiller; Saatvik Agarwal; James H Notwell; Ravi Parikh; Harendra Guturu; Aaron M Wenger; Gill Bejerano
Journal: Nucleic Acids Res Date: 2013-06-27 Impact factor: 16.971

Review 10. The mystery of extreme non-coding conservation.

Authors: Nathan Harmston; Anja Baresic; Boris Lenhard
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2013-11-11 Impact factor: 6.237