Xenbase: gene expression and improved integration

被引：97

作者：

Bowes, Jeff B. ^{[1
]}

Snyder, Kevin A. ^{[1
]}

Segerdell, Erik ^{[1
]}

Jarabek, Chris J. ^{[1
]}

Azam, Kenan ^{[1
]}

Zorn, Aaron M. ^{[2
,3
]}

Vize, Peter D. ^{[1
]}

机构：

[1] Univ Calgary, Dept Biol Sci, Calgary, AB, Canada

[2] Cincinnati Childrens Res Fdn, Div Dev Biol, Cincinnati, OH 45229 USA

[3] Univ Cincinnati, Dept Pediat, Coll Med, Cincinnati, OH 45229 USA

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

XENOPUS-LAEVIS; EVOLUTION; DATABASE;

D O I：

10.1093/nar/gkp953

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog pages. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. The gene catalog has grown to contain over 15 000 genes. Collaboration with the European Xenopus Research Center (EXRC) has resulted in a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and the clearing-house for Xenopus gene nomenclature.

引用

页码：D607 / D612

页数：6

共 10 条

[1] NCBI GEO: archive for high-throughput functional genomic data [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Rudnev, Dmitry ;

Evangelista, Carlos ;

Kim, Irene F. ;

Soboleva, Alexandra ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Edgar, Ron .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D885-D890

[2] Xenbase:: a Xenopus biology and genomics resource [J].

Bowes, Jeff B. ;

Snyder, Kevin A. ;

Segerdell, Erik ;

Gibb, Ross ;

Jarabek, Chris ;

Noumen, Etienne ;

Pollet, Nicolas ;

Vize, Peter D. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D761-D767

[3] Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization [J].

Chain, Frederic J. J. ;

Ilieva, Dora ;

Evans, Ben J. .

BMC EVOLUTIONARY BIOLOGY, 2008, 8 (1)

[4] Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data [J].

Gilchrist, Michael J. ;

Christensen, Mikkel B. ;

Harland, Richard ;

Pollet, Nicolas ;

Smith, James C. ;

Ueno, Naoto ;

Papalopulu, Nancy .

BMC BIOINFORMATICS, 2008, 9 (1) :442

[5] Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis [J].

Hellsten, Uffe ;

Khokha, Mustafa K. ;

Grammer, Timothy C. ;

Harland, Richard M. ;

Richardson, Paul ;

Rokhsar, Daniel S. .

BMC BIOLOGY, 2007, 5 (1)

[6] Ensembl 2009 [J].

Hubbard, T. J. P. ;

Aken, B. L. ;

Ayling, S. ;

Ballester, B. ;

Beal, K. ;

Bragin, E. ;

Brent, S. ;

Chen, Y. ;

Clapham, P. ;

Clarke, L. ;

Coates, G. ;

Fairley, S. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Gordon, L. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. ;

Jenkinson, A. ;

Johnson, N. ;

Kahari, A. ;

Keefe, D. ;

Keenan, S. ;

Kinsella, R. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Rios, D. ;

Schuster, M. ;

Slater, G. ;

Smedley, D. ;

Spooner, W. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. ;

Vogel, J. ;

White, S. ;

Wilder, S. ;

Zadissa, A. ;

Birney, E. ;

Cunningham, F. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D690-D697

[7]

Nieuwkoop PD., 1994, Normal Table of Xenopus Laevis (Daudin): A Systematical and Chronological Survey of the Development from the Fertilized Egg Till the End of Metamorphosis, DOI DOI 10.1201/9781003064565

[8] Axeldb:: a Xenopus laevis database focusing on gene expression [J].

Pollet, N ;

Schmidt, HA ;

Gawantka, V ;

Vingron, M ;

Niehrs, C .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :139-140

[9] An ontology for Xenopus anatomy and development [J].

Segerdell, Erik ;

Bowes, Jeff B. ;

Pollet, Nicolas ;

Vize, Peter D. .

BMC DEVELOPMENTAL BIOLOGY, 2008, 8

[10] The Generic Genome Browser: A building block for a model organism system database [J].

Stein, LD ;

Mungall, C ;

Shu, SQ ;

Caudy, M ;

Mangone, M ;

Day, A ;

Nickerson, E ;

Stajich, JE ;

Harris, TW ;

Arva, A ;

Lewis, S .

GENOME RESEARCH, 2002, 12 (10) :1599-1610

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