Omics databases in plant science: key to systems biology

被引：9

作者：

Suwabe, Keita ^{[1
]}

Yano, Kentaro ^{[2
]}

机构：

[1] Tohoku Univ, Grad Sch Life Sci, Sendai, Miyagi 9808577, Japan

[2] Meiji Univ, Fac Agr, Kawasaki Ku, Kanagawa 2148571, Japan

来源：

PLANT BIOTECHNOLOGY | 2008年 / 25卷 / 05期

关键词：

Bioinformatics; database; genome sequence; Internet; omics;

D O I：

10.5511/plantbiotechnology.25.413

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：

Recently, high-throughput technologies for comprehensive genomic, transcriptomic and proteomic analyses have been developed. Large-scale 'omics data' obtained from such experimental methods have rapidly accumulated and been stored into web databases. In addition, the number of web databases for molecular biology has rapidly increased, since most new projects construct and maintain new web databases for their own large-scale omics data. This wealth of comprehensive online resources and web databases allow us to extract essential new biological information beyond a dataset obtained from an individual study. For effective and efficient handling of such large sets of data, various kinds of bioinformatics tools are being developed. Here, we review the current state of web databases and bioinformatics tools for plant biosciences and systems biology.

引用

页码：413 / 422

页数：10

共 45 条

[1]

AOKI K, 2007, ACTA HORTIC, V745, P457

[2] The Molecular Biology Database Collection: an updated compilation of biological database resources [J].

Baxevanis, AD .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :1-10

[3]

Benson DA, 2010, NUCLEIC ACIDS RES, V38, pD46, DOI [10.1093/nar/gkp1024, 10.1093/nar/gkq1079, 10.1093/nar/gkl986, 10.1093/nar/gks1195, 10.1093/nar/gkw1070, 10.1093/nar/gkr1202, 10.1093/nar/gkn723, 10.1093/nar/gkx1094]

[4] DBEST - DATABASE FOR EXPRESSED SEQUENCE TAGS [J].

BOGUSKI, MS ;

LOWE, TMJ ;

TOLSTOSHEV, CM .

NATURE GENETICS, 1993, 4 (04) :332-333

[5]

Brunak S, 2002, SCIENCE, V298, P1333

[6]

*CEN ONT CONS, 2008, NUCLEIC ACIDS RES, V36, pD440

[7] Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database [J].

Cochrane, Guy ;

Akhtar, Ruth ;

Aldebert, Philippe ;

Althorpe, Nicola ;

Baldwin, Alastair ;

Bates, Kirsty ;

Bhattacharyya, Sumit ;

Bonfield, James ;

Bower, Lawrence ;

Browne, Paul ;

Castro, Matias ;

Cox, Tony ;

Demiralp, Fehmi ;

Eberhardt, Ruth ;

Faruque, Nadeem ;

Hoad, Gemma ;

Jang, Mikyung ;

Kulikova, Tamara ;

Labarga, Alberto ;

Leinonen, Rasko ;

Leonard, Steven ;

Lin, Quan ;

Lopez, Rodrigo ;

Lorenc, Dariusz ;

McWilliam, Hamish ;

Mukherjee, Gaurab ;

Nardone, Francesco ;

Plaister, Sheila ;

Robinson, Stephen ;

Sobhany, Siamak ;

Vaughan, Robert ;

Wu, Dan ;

Zhu, Weimin ;

Apweiler, Rolf ;

Hubbard, Tim ;

Birney, Ewan .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D5-D12

[8] NCBI GEO standards and services for microarray data [J].

Edgar, Ron ;

Barrett, Tanya .

NATURE BIOTECHNOLOGY, 2006, 24 (12) :1471-1472

[9] Cluster analysis and display of genome-wide expression patterns [J].

Eisen, MB ;

Spellman, PT ;

Brown, PO ;

Botstein, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) :14863-14868

[10] Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression [J].

Ewing, RM ;

Ben Kahla, A ;

Poirot, O ;

Lopez, F ;

Audic, S ;

Claverie, JM .

GENOME RESEARCH, 1999, 9 (10) :950-959

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