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      MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

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          Abstract

          MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP.

          Abstract

          MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP http://www.GenMAPP.org. The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Creating the gene ontology resource: design and implementation.

            (2001)
            The exponential growth in the volume of accessible biological information has generated a confusion of voices surrounding the annotation of molecular information about genes and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular component, and providing a community database resource that supports the use of these ontologies. The GO Consortium was initiated by scientists associated with three model organism databases: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases. Additional model organism database groups are joining the project. Each of these model organism information systems is annotating genes and gene products using GO vocabulary terms and incorporating these annotations into their respective model organism databases. Each database contributes its annotation files to a shared GO data resource accessible to the public at http://www.geneontology.org/. The GO site can be used by the community both to recover the GO vocabularies and to access the annotated gene product data sets from the model organism databases. The GO Consortium supports the development of the GO database resource and provides tools enabling curators and researchers to query and manipulate the vocabularies. We believe that the shared development of this molecular annotation resource will contribute to the unification of biological information.
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              GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways.

              Kam D Dahlquist, Nathan Salomonis, Karen Vranizan … (2002)
              Article 0 comments Cited 218 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2003
                Publication date (Electronic): 6 January 2003
                Volume: 4
                Issue: 1
                Page: R7
                Affiliations
                [1 ]Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141-9100, USA
                [2 ]Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
                [3 ]Departments of Medicine and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
                [4 ]Functional Genomics Lab, University of California, Berkeley, CA 94720, USA
                Correspondence: Bruce R Conklin. E-mail: bconklin@gladstone.ucsf.edu
                Article
                Publisher ID: gb-2003-4-1-r7
                DOI: 10.1186/gb-2003-4-1-r7
                PMC ID: 151291
                PubMed ID: 12540299
                SO-VID: 23cafc1a-5362-4761-8021-0e75eb3a7ced
                Copyright © Copyright © 2003 Doniger et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
                History
                Date received : 11 September 2002
                Date revision received : 8 October 2002
                Date accepted : 8 November 2002
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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