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WEGO: a web tool for plotting GO annotations

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      Abstract

      Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@ 123456genomics.org.cn .

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      Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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        The Gene Ontology (GO) database and informatics resource.

        The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
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          GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

          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. The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/.
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            Author and article information

            Affiliations
            1simpleJames D. Watson Institute of Genome Sciences of Zhejiang University Hangzhou 310008, China
            2simpleBeijing Genomics Institute Beijing 101300, China
            3simpleCollege of Life Sciences, Peking University Beijing 100871, China
            4simpleThe Institute of Human Genetics, University of Aarhus DK-8000 Aarhus C, Denmark
            5simpleDepartment of Biochemistry and Molecular Biology, University of Southern Denmark DK-5230, Odense M, Denmark
            Author notes
            *To whom correspondence should be addressed. Tel: +86 10 80491664; Fax: +86 10 80498676; Email: wangj@ 123456genomics.org.cn
            Correspondence may also be addressed to Lars Bolund. Tel: +45 89421675; Fax: +45 86123173; Email: bolund@ 123456humgen.au.dk

            The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

            Journal
            Nucleic Acids Res
            Nucleic Acids Research
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            01 July 2006
            01 July 2006
            14 July 2006
            : 34
            : Web Server issue
            : W293-W297
            1538768
            10.1093/nar/gkl031
            16845012
            © The Author 2006. Published by Oxford University Press. All rights reserved

            The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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            Genetics

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