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

[1] The genome sequence of Drosophila melanogaster
Adams, MD
Celniker, SE
Holt, RA
Evans, CA
Gocayne, JD
Amanatides, PG
Scherer, SE
Li, PW
Hoskins, RA
Galle, RF
George, RA
Lewis, SE
Richards, S
Ashburner, M
Henderson, SN
Sutton, GG
Wortman, JR
Yandell, MD
Zhang, Q
Chen, LX
Brandon, RC
Rogers, YHC
Blazej, RG
Champe, M
Pfeiffer, BD
Wan, KH
Doyle, C
Baxter, EG
Helt, G
Nelson, CR
Miklos, GLG
Abril, JF
Agbayani, A
An, HJ
Andrews-Pfannkoch, C
Baldwin, D
Ballew, RM
Basu, A
Baxendale, J
Bayraktaroglu, L
Beasley, EM
Beeson, KY
Benos, PV
Berman, BP
Bhandari, D
Bolshakov, S
Borkova, D
Botchan, MR
Bouck, J
Brokstein, P
[J]. SCIENCE, 2000, 287 (5461) : 2185 - 2195
[2] Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
Alexa, Adrian
Rahnenfuehrer, Joerg
Lengauer, Thomas
[J]. BIOINFORMATICS, 2006, 22 (13) : 1600 - 1607
[3] Ashburner M, 2001, GENOME RES, V11, P1425
[4] Gene Ontology: tool for the unification of biology
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
[J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
[5] Ontologies in biology: Design, applications and future challenges
Bard, JBL
Rhee, SY
[J]. NATURE REVIEWS GENETICS, 2004, 5 (03) : 213 - 222
[6] Lowest common ancestors in trees and directed acyclic graphs
Bender, MA
Farach-Colton, M
Pemmasani, G
Skiena, S
Sumazin, P
[J]. JOURNAL OF ALGORITHMS-COGNITION INFORMATICS AND LOGIC, 2005, 57 (02): : 75 - 94
[7] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING
BENJAMINI, Y
HOCHBERG, Y
[J]. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) : 289 - 300
[8] Stamen abscission zone transcriptome profiling reveals new candidates for abscission control:: Enhanced retention of floral organs in Transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2
Cai, Suqin
Lashbrook, Coralie C.
[J]. PLANT PHYSIOLOGY, 2008, 146 (03) : 1305 - 1321
[9] Camon EB, 2005, BMC BIOINFORMATICS, V6, DOI 10.1186/1471-2105-6-S1-S17
[10] Camon Evelyn, 2004, In Silico Biology, V4, P5

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