Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%

被引：44

作者：

Aslett, Martin ^{[1
]}

Wood, Valerie ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1HH, England

来源：

YEAST | 2006年 / 23卷 / 13期

关键词：

gene ontology; Schizosaccharomyces; pombe; annotation; curation; reference genome; fission yeast;

D O I：

10.1002/yea.1420

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：

In this review, we present an overview of the Gene Ontology (GO) structure and describe how the GO is implemented for Sz. pombe and made available via Sz. pombe GeneDB (http://www.genedb.org/genedb/pombe/). We give a detailed progress report of Sz. pombe GO annotation, providing the current status of both manual and automatic annotations. Fission yeast has at least one GO annotation for 98.3% of its genes (excluding annotations to 'unknown' terms), greater than the current percentage coverage for any other organism. Approximately 65% (3225 gene products) have at least one annotation to each of the three ontologies (biological process, cellular component and molecular function). Approximately 30% (1443 gene products) have GO terms derived directly from small-scale experiments in fission yeast, supporting the validity of fission yeast as a model eukaryote and a reference organism. Copyright (c) 2006 John Wiley & Sons, Ltd.

引用

页码：913 / 919

页数：7

共 8 条

[1]

Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkw1099, 10.1093/nar/gkh131]

[2] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[3] The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology [J].

Camon, E ;

Magrane, M ;

Barrell, D ;

Lee, V ;

Dimmer, E ;

Maslen, J ;

Binns, D ;

Harte, N ;

Lopez, R ;

Apweiler, R .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D262-D266

[4]

G. O. Consortium, 2004, Nucleic Acids Res, V32, pD258, DOI DOI 10.1093/NAR/GKH036

[5] GeneDB: a resource for prokaryotic and eukaryotic organisms [J].

Hertz-Fowler, C ;

Peacock, CS ;

Wood, V ;

Aslett, M ;

Kerhornou, A ;

Mooney, P ;

Tivey, A ;

Berriman, M ;

Hall, N ;

Rutherford, K ;

Parkhill, J ;

Ivens, AC ;

Rajandream, MA ;

Barrell, B .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D339-D343

[6] The role of lineage-specific gene family expansion in the evolution of eukaryotes [J].

Lespinet, O ;

Wolf, YI ;

Koonin, EV ;

Aravind, L .

GENOME RESEARCH, 2002, 12 (07) :1048-1059

[7] ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe [J].

Matsuyama, Akihisa ;

Arai, Ritsuko ;

Yashiroda, Yoko ;

Shirai, Atsuko ;

Kamata, Ayako ;

Sekido, Shigeko ;

Kobayashi, Yumiko ;

Hashimoto, Atsushi ;

Hamamoto, Makiko ;

Hiraoka, Yasushi ;

Horinouchi, Sueharu ;

Yoshida, Minoru .

NATURE BIOTECHNOLOGY, 2006, 24 (07) :841-847

[8]

WOOD V, 2006, COMP GENOMICS USING

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