Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.
Applications Note |
GOstat: find statistically overrepresented Gene Ontologies within a group of genes
Walter and Eliza Hall Institute of medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia
Received on July 14, 2004; revised on December 1, 2003; accepted on December 4, 2003
Advance Access Publication February 12, 2004
Summary: Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the analyzed process. In order to gain biological understanding from this type of data, it is necessary to analyze the functional annotations of all genes in this list. The Gene-Ontology (GO) database provides a useful tool to annotate and analyze the functions of a large number of genes. Here, we introduce a tool that utilizes this information to obtain an understanding of which annotations are typical for the analyzed list of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are overrepresented in the analyzed list of genes. This results in a list of GO terms sorted by their specificity.
Availability: Our program GOstat is accessible via the Internet at http://gostat.wehi.edu.au
Contact: beissbarth{at}wehi.edu.au
* To whom correspondence should be addressed.
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X. Yu, W. C. Griffith, K. Hanspers, J. F. Dillman III, H. Ong, M. A. Vredevoogd, and E. M. Faustman A System-Based Approach to Interpret Dose- and Time-Dependent Microarray Data: Quantitative Integration of Gene Ontology Analysis for Risk Assessment Toxicol. Sci., August 1, 2006; 92(2): 560 - 577. [Abstract] [Full Text] [PDF]
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J. A. Fulcher, S. T. Hashimi, E. L. Levroney, M. Pang, K. B. Gurney, L. G. Baum, and B. Lee Galectin-1-Matured Human Monocyte-Derived Dendritic Cells Have Enhanced Migration through Extracellular Matrix J. Immunol., July 1, 2006; 177(1): 216 - 226. [Abstract] [Full Text] [PDF]
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M. Kankainen, P. Pehkonen, P. Rosenstom, P. Toronen, G. Wong, and L. Holm POXO: a web-enabled tool series to discover transcription factor binding sites. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W534 - W540. [Abstract] [Full Text] [PDF]
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J. Wu, X. Mao, T. Cai, J. Luo, and L. Wei KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W720 - W724. [Abstract] [Full Text] [PDF]
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A. Alexa, J. Rahnenfuhrer, and T. Lengauer Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics, July 1, 2006; 22(13): 1600 - 1607. [Abstract] [Full Text] [PDF]
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M. Beller, D. Riedel, L. Jansch, G. Dieterich, J. Wehland, H. Jackle, and R. P. Kuhnlein Characterization of the Drosophila Lipid Droplet Subproteome Mol. Cell. Proteomics, June 1, 2006; 5(6): 1082 - 1094. [Abstract] [Full Text] [PDF]
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M. Blanchette, A. R. Bataille, X. Chen, C. Poitras, J. Laganiere, C. Lefebvre, G. Deblois, V. Giguere, V. Ferretti, D. Bergeron, et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression Genome Res., May 1, 2006; 16(5): 656 - 668. [Abstract] [Full Text] [PDF]
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J. Tuikkala, L. Elo, O. S. Nevalainen, and T. Aittokallio Improving missing value estimation in microarray data with gene ontology Bioinformatics, March 1, 2006; 22(5): 566 - 572. [Abstract] [Full Text] [PDF]
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