Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2004 20(18):3710-3715; doi:10.1093/bioinformatics/bth456
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
Applications Note |
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
1 Department of Genetics and 2 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
Received on August 5, 2003; revised on May 10, 2004; accepted on June 29, 2004
Advance Access Publication August 5, 2004
Summary: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.
Availability: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/
Contact: sherlock{at}genome.stanford.edu
* To whom correspondence should be addressed.
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|
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|
|
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|
|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 M. Y. Park, T. Hastie, and R. Tibshirani Averaged gene expressions for regression Biostat., April 1, 2007; 8(2): 212 - 227. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
J. Demeter, C. Beauheim, J. Gollub, T. Hernandez-Boussard, H. Jin, D. Maier, J. C. Matese, M. Nitzberg, F. Wymore, Z. K. Zachariah, et al. The Stanford Microarray Database: implementation of new analysis tools and open source release of software Nucleic Acids Res., January 12, 2007; 35(suppl_1): D766 - D770. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
Y. Zhang, X. S. Liu, Q.-R. Liu, and L. Wei Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species Nucleic Acids Res., July 18, 2006; 34(12): 3465 - 3475. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
J. Ye, L. Fang, H. Zheng, Y. Zhang, J. Chen, Z. Zhang, J. Wang, S. Li, R. Li, L. Bolund, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W293 - W297. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Scheer, F. Klawonn, R. Munch, A. Grote, K. Hiller, C. Choi, I. Koch, M. Schobert, E. Hartig, U. Klages, et al. JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W510 - W515. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
B. Adamcsek, G. Palla, I. J. Farkas, I. Derenyi, and T. Vicsek CFinder: locating cliques and overlapping modules in biological networks Bioinformatics, April 15, 2006; 22(8): 1021 - 1023. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 L. M. Helvering, R. Liu, N. H. Kulkarni, T. Wei, P. Chen, S. Huang, F. Lawrence, D. L. Halladay, R. R. Miles, E. M. Ambrose, et al. Expression Profiling of Rat Femur Revealed Suppression of Bone Formation Genes by Treatment with Alendronate and Estrogen but Not Raloxifene Mol. Pharmacol., November 1, 2005; 68(5): 1225 - 1238. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Conesa, R. Ruotolo, P. Soularue, T. A. Simms, D. Donze, A. Sentenac, and G. Dieci Modulation of Yeast Genome Expression in Response to Defective RNA Polymerase III-Dependent Transcription Mol. Cell. Biol., October 1, 2005; 25(19): 8631 - 8642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary Bioinformatics, October 1, 2005; 21(19): 3787 - 3793. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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