Use and misuse of the gene ontology annotations

被引：345

作者：

Rhee, Seung Yon ^{[1
]}

Wood, Valerie ^{[2
]}

Dolinski, Kara ^{[3
]}

Draghici, Sorin ^{[4
]}

机构：

[1] Carnegie Inst Sci, Dept Plant Biol, Stanford, CA 94305 USA

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[3] Princeton Univ, Carl Icahn Lab, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA

[4] Wayne State Univ, Dept Comp Sci, Detroit, MI 48202 USA

来源：

NATURE REVIEWS GENETICS | 2008年 / 9卷 / 07期

关键词：

D O I：

10.1038/nrg2363

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The Gene Ontology (GO) project is a collaboration among model organism databases to describe gene products from all organisms using a consistent and computable language. GO produces sets of explicitly defined, structured vocabularies that describe biological processes, molecular functions and cellular components of gene products in both a computer-and human-readable manner. Here we describe key aspects of GO, which, when overlooked, can cause erroneous results, and address how these pitfalls can be avoided.

引用

页码：509 / 515

页数：7

共 41 条

[21] Functional annotation of a full-length mouse cDNA collection [J].

Kawai, J ;

Shinagawa, A ;

Shibata, K ;

Yoshino, M ;

Itoh, M ;

Ishii, Y ;

Arakawa, T ;

Hara, A ;

Fukunishi, Y ;

Konno, H ;

Adachi, J ;

Fukuda, S ;

Aizawa, K ;

Izawa, M ;

Nishi, K ;

Kiyosawa, H ;

Kondo, S ;

Yamanaka, I ;

Saito, T ;

Okazaki, Y ;

Gojobori, T ;

Bono, H ;

Kasukawa, T ;

Saito, R ;

Kadota, K ;

Matsuda, H ;

Ashburner, M ;

Batalov, S ;

Casavant, T ;

Fleischmann, W ;

Gaasterland, T ;

Gissi, C ;

King, B ;

Kochiwa, H ;

Kuehl, P ;

Lewis, S ;

Matsuo, Y ;

Nikaido, I ;

Pesole, G ;

Quackenbush, J ;

Schriml, LM ;

Staubli, F ;

Suzuki, R ;

Tomita, M ;

Wagner, L ;

Washio, T ;

Sakai, K ;

Okido, T ;

Furuno, M ;

Aono, H .

NATURE, 2001, 409 (6821) :685-690

[22] Ontological analysis of gene expression data: current tools, limitations, and open problems [J].

Khatri, P ;

Draghici, S .

BIOINFORMATICS, 2005, 21 (18) :3587-3595

[23] A semantic analysis of the annotations of the human genome [J].

Khatri, P ;

Done, B ;

Rao, A ;

Done, A ;

Draghici, S .

BIOINFORMATICS, 2005, 21 (16) :3416-3421

[24] Gene expression profiles of genistein-treated PC3 prostate cancer cells [J].

Li, YW ;

Sarkar, FH .

JOURNAL OF NUTRITION, 2002, 132 (12) :3623-3631

[25] Network-based analysis of affected biological processes in type 2 diabetes models [J].

Liu, Manway ;

Liberzon, Arthur ;

Kong, Sek Won ;

Lai, Weil R. ;

Park, Peter J. ;

Kohane, Isaac S. ;

Kasif, Simon .

PLOS GENETICS, 2007, 3 (06) :958-972

[26] POWER_SAGE: comparing statistical tests for SAGE experiments [J].

Man, MZ ;

Wang, XN ;

Wang, YX .

BIOINFORMATICS, 2000, 16 (11) :953-959

[27]

Marcotte E, 2001, Brief Bioinform, V2, P363, DOI 10.1093/bib/2.4.363

[28] Computational identification of cellular networks and pathways [J].

Markowetz, Florian ;

Troyanskaya, Olga G. .

MOLECULAR BIOSYSTEMS, 2007, 3 (07) :478-482

[29] GOing from functional genomics to biological significance [J].

McCarthy, F. M. ;

Bridges, S. M. ;

Burgess, S. C. .

CYTOGENETIC AND GENOME RESEARCH, 2007, 117 (1-4) :278-287

[30] Finding function: evaluation methods for functional genomic data [J].

Myers, Chad L. ;

Barrett, Daniel R. ;

Hibbs, Matthew A. ;

Huttenhower, Curtis ;

Troyanskaya, Olga G. .

BMC GENOMICS, 2006, 7 (1)

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