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

被引：67

作者：

Engstrom, Paer G. ^{[1
,2
,3
]}

Fredman, David ^{[1
,2
]}

Lenhard, Boris ^{[1
,2
]}

机构：

[1] Univ Bergen, Bergen Ctr Computat Sci, Computat Biol Unit, N-5008 Bergen, Norway

[2] Univ Bergen, Sars Ctr Marine Mol Biol, N-5008 Bergen, Norway

[3] Karolinska Inst, Dept Cell & Mol Biol, Programme Genom & Bioinformat, S-17177 Stockholm, Sweden

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 02期

关键词：

D O I：

10.1186/gb-2008-9-2-r34

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Metazoan genomes contain arrays of highly conserved noncoding elements (HCNEs) that span developmental regulatory genes and define regulatory domains. We describe Ancora http://ancora.genereg.net, a web resource that provides data and tools for exploring genomic organization of HCNEs for multiple genomes. Ancora includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains.

引用

页数：12

共 45 条

[1] Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny [J].

Ahituv, N ;

Prabhakar, S ;

Rubin, EM ;

Couronne, O .

HUMAN MOLECULAR GENETICS, 2005, 14 (20) :3057-3063

[2] Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes [J].

Aparicio, S ;

Chapman, J ;

Stupka, E ;

Putnam, N ;

Chia, J ;

Dehal, P ;

Christoffels, A ;

Rash, S ;

Hoon, S ;

Smit, A ;

Gelpke, MDS ;

Roach, J ;

Oh, T ;

Ho, IY ;

Wong, M ;

Detter, C ;

Verhoef, F ;

Predki, P ;

Tay, A ;

Lucas, S ;

Richardson, P ;

Smith, SF ;

Clark, MS ;

Edwards, YJK ;

Doggett, N ;

Zharkikh, A ;

Tavtigian, SV ;

Pruss, D ;

Barnstead, M ;

Evans, C ;

Baden, H ;

Powell, J ;

Glusman, G ;

Rowen, L ;

Hood, L ;

Tan, YH ;

Elgar, G ;

Hawkins, T ;

Venkatesh, B ;

Rokhsar, D ;

Brenner, S .

SCIENCE, 2002, 297 (5585) :1301-1310

[3] The random versus fragile breakage models of chromosome evolution: a matter of resolution [J].

Becker, Thomas S. ;

Lenhard, Boris .

MOLECULAR GENETICS AND GENOMICS, 2007, 278 (05) :487-491

[4] Ultraconserved elements in the human genome [J].

Bejerano, G ;

Pheasant, M ;

Makunin, I ;

Stephen, S ;

Kent, WJ ;

Mattick, JS ;

Haussler, D .

SCIENCE, 2004, 304 (5675) :1321-1325

[5] Multiple whole genome alignments and novel biomedical applications at the VISTA portal [J].

Brudno, Michael ;

Poliakov, Alexander ;

Minovitsky, Simon ;

Ratnere, Igor ;

Dubchak, Inna .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W669-W674

[6] Skeletal muscle progenitor cells and the role of Pax genes [J].

Buckingham, Margaret .

COMPTES RENDUS BIOLOGIES, 2007, 330 (6-7) :530-533

[7]

Celniker Susan., 2002, GENOME BIOL, V3, DOI [10.1186/gb-2002-3-12-research0079, DOI 10.1186/GB-2002-3-12-RESEARCH0079]

[8] Evolution of genes and genomes on the Drosophila phylogeny [J].

Clark, Andrew G. ;

Eisen, Michael B. ;

Smith, Douglas R. ;

Bergman, Casey M. ;

Oliver, Brian ;

Markow, Therese A. ;

Kaufman, Thomas C. ;

Kellis, Manolis ;

Gelbart, William ;

Iyer, Venky N. ;

Pollard, Daniel A. ;

Sackton, Timothy B. ;

Larracuente, Amanda M. ;

Singh, Nadia D. ;

Abad, Jose P. ;

Abt, Dawn N. ;

Adryan, Boris ;

Aguade, Montserrat ;

Akashi, Hiroshi ;

Anderson, Wyatt W. ;

Aquadro, Charles F. ;

Ardell, David H. ;

Arguello, Roman ;

Artieri, Carlo G. ;

Barbash, Daniel A. ;

Barker, Daniel ;

Barsanti, Paolo ;

Batterham, Phil ;

Batzoglou, Serafim ;

Begun, Dave ;

Bhutkar, Arjun ;

Blanco, Enrico ;

Bosak, Stephanie A. ;

Bradley, Robert K. ;

Brand, Adrianne D. ;

Brent, Michael R. ;

Brooks, Angela N. ;

Brown, Randall H. ;

Butlin, Roger K. ;

Caggese, Corrado ;

Calvi, Brian R. ;

de Carvalho, A. Bernardo ;

Caspi, Anat ;

Castrezana, Sergio ;

Celniker, Susan E. ;

Chang, Jean L. ;

Chapple, Charles ;

Chatterji, Sourav ;

Chinwalla, Asif ;

Civetta, Alberto .

NATURE, 2007, 450 (7167) :203-218

[9] A mouse model for human short-stature syndromes identifies Shox2 as an upstream regulator of Runx2 during long-bone development [J].

Cobb, J ;

Dierich, A ;

Huss-Garcia, Y ;

Duboule, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (12) :4511-4515

[10] FlyBase: genomes by the dozen [J].

Crosby, Madeline A. ;

Goodman, Joshua L. ;

Strelets, Victor B. ;

Zhang, Peili ;

Gelbart, William M. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D486-D491

← 1 2 3 4 5 →