Use and misuse of the gene ontology annotations

被引：340

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
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
[J]. NATURE, 2001, 409 (6821) : 685 - 690
[22] Ontological analysis of gene expression data: current tools, limitations, and open problems
Khatri, P
Draghici, S
[J]. BIOINFORMATICS, 2005, 21 (18) : 3587 - 3595
[23] A semantic analysis of the annotations of the human genome
Khatri, P
Done, B
Rao, A
Done, A
Draghici, S
[J]. BIOINFORMATICS, 2005, 21 (16) : 3416 - 3421
[24] Gene expression profiles of genistein-treated PC3 prostate cancer cells
Li, YW
Sarkar, FH
[J]. JOURNAL OF NUTRITION, 2002, 132 (12) : 3623 - 3631
[25] Network-based analysis of affected biological processes in type 2 diabetes models
Liu, Manway
Liberzon, Arthur
Kong, Sek Won
Lai, Weil R.
Park, Peter J.
Kohane, Isaac S.
Kasif, Simon
[J]. PLOS GENETICS, 2007, 3 (06): : 958 - 972
[26] POWER_SAGE: comparing statistical tests for SAGE experiments
Man, MZ
Wang, XN
Wang, YX
[J]. 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
Markowetz, Florian
Troyanskaya, Olga G.
[J]. MOLECULAR BIOSYSTEMS, 2007, 3 (07) : 478 - 482
[29] GOing from functional genomics to biological significance
McCarthy, F. M.
Bridges, S. M.
Burgess, S. C.
[J]. CYTOGENETIC AND GENOME RESEARCH, 2007, 117 (1-4) : 278 - 287
[30] Finding function: evaluation methods for functional genomic data
Myers, Chad L.
Barrett, Daniel R.
Hibbs, Matthew A.
Huttenhower, Curtis
Troyanskaya, Olga G.
[J]. BMC GENOMICS, 2006, 7 (1)

← 1 2 3 4 5 →