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GO Tools: Editors, Browsers, General GO tools and Other Tools
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We're interested in bringing together parts which software developers think are useful, somewhat documented and portable. If there are any resources that you would like to see on this page then please contact the webmaster at go@geneontology.org. If you have been involved in the writing of any tools that work with GO then please write to us with information about your tool. The main details that we are looking for are listed on the Submit New Tools page. To see the information that has already been collected, visit the GO Tools Developers' Site.
Click here to send information about your tools, or e-mail go@geneontology.org.
Gene Ontology Editors
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DAG-Edit
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This Java application provides an interface to browse, query and edit GO or any other vocabulary that has a DAG data structure. The most current version of DAG-Edit can be downloaded from the publicly accessible source repository at SourceForge. Help documentation is now included in the program, or is avaliable here: dagedit_userguide/dagedit. html
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GO Browsers
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AmiGO from BDGP
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With AmiGO, you can search for a GO term and view all gene products annotated to it, or search for a gene product and view all its associations. You can also browse the ontologies to view relationships between terms as well as the number of gene products annotated to a given term. AmiGO accesses the GO mySQL database (see below); the browser and documentation are available from http://www.godatabase.org/dev/
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MGI GO Browser
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With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the term or any subterms. You can also browse the ontologies to view relationships between terms, term definitions, as well as the number of mouse genes annotated to a given term and its subterms. The MGI GO browser directly accesses the GO in the MGI database where mouse gene annotations, are updated nightly. The version of the GO used is obtained nightly from the GO ftp site.
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QuickGO at EBI
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With QuickGO, a GO browser integrated into InterPro at the EBI, you can search for a GO term to see its relationships and definition, as well as any available mappings to SWISS-PROT keywords, to the Enzyme Classification or Transport Classification databases, or to InterPro entries. Use documentation is available from the manual and the FAQ.
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EP GO Browser
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The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.
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GoFish
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The GoFish program, available as a Java applet, allows the user to construct arbitrary Boolean queries using GO attributes, and orders gene products according to the extent they satisfy such queries. GoFish also estimates, for each gene product, the probability that they satisfy the Boolean query. Developed by the Roth lab at Harvard.
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GenNav
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GenNav is a GO browser developed at NLM. It searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.
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GeneOntology@RZPD
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With the GeneOntology@RZPD tool at the Resource Center/Primary Database (RZPD) in Germany, you can search for GO identifiers associated with UniGene ClusterIds, Genes (Name/Symbol) and Clones provided by the RZPD. You can also search for UniGene Clusters, Genes and Clones annotated with a certain GO identifier or a combination of GO identifiers. So far, GO annotations for human and mouse genes/clones are linked.
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ProToGO
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ProToGO, developed at the Hebrew University in Jerusalem, searches the GOA@EBI and Compugen annotation datasets. The output is a graphical view of the relevant sub-graph of GO, containing those GO terms assigned to the query proteins. Documentation is provided.
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CGAP GO Browser
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With the GO browser at the The Cancer Genome Anatomy Project, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. The help documentation is at: http://cgap.nci.nih.gov/Genes/AllAboutGO.
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GOBrowser
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GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. Click 'download tarball' at the bioperl.org cvs site to download the programme. All available documentation is included in this download. GOBrowser was written by Mark Wilkinson of Illuminae.
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TAIR Keyword Browser
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TAIR Keyword Browser , developed at The Arabidopsis Information Resource searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms.
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PANDORA
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With PANDORA , developed at The Hebrew University of Jerusalem you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from SwissProt, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families.
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Other GO Tools
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GO Term Finder
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The GO Term Finder searches for significant shared GO terms, or parents of the GO terms, used to annotate gene products in a given list. A web-based GO Term Finder at SGD searches annotations of budding yeast gene products. A generic GO Term Finder has been created by SMD and can be downloaded from CPAN.
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GO Term Mapper
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The GO Term Mapper at SGD maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding GO Slim terms (i.e. more general parent GO terms; uses the SGD GO Slim set).
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MAPPFinder
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MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest.
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FatiGO
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FatiGO is a web-based tool, from the Bioinformatics unit at the CNIO (Spain), that assigns representative functional information (under-represented or over-represented Gene Ontology terms) to a given set of genes. Statistical significance is obtained using multiple-testing correction. FatiGO has been designed for functional annotation in the context of DNA microarray data analysis, and is linked to the GEPAS. FatiGO uses gene IDs from the major genomic and proteomic databases (GeneBank, SWISS-PROT/TREMBL, Unigene, Ensembl, etc.)
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GoMiner & MatchMiner
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GoMiner is a Java-based program package that organizes lists of 'interesting' genes (e.g., up- and down-regulated genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations: (i) a tree-like structure analogous to that in the AmiGO browser and (ii) a compact, dynamically interactive DAG. Genes displayed in GoMiner are linked to major public bioinformatics resources. A companion tool, MatchMiner, can be used as a preprocessor to obtain gene names for input to GoMiner or other GO tools.
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OntoGate
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OntoGate provides access to GenomeMatrix (GM) entries from Ontology terms and external datasets which have been associated with ontology terms, to find genes from different species in the GM, which have been mapped to the ontology terms. OntoGate includes a BLAST search of amino acid sequences corresponding to annotated genes.
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Onto-Express
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Onto-Express translates lists of genes found to be differentially regulated in high throughput gene expression experiments, into functional profiles based on GO. The statistical significance value is calculated, and results are graphically displayed as bar graphs and pie charts as well as GO hierarchical trees. Onto-Express is available from the Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
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Onto-Design
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Onto-Design allows the user to design custom microarrays by selecting a set of UniGene cluster IDs that represent a given subset of biological processes described using GO terms. Onto-Design is available from the Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
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Onto-Compare
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Onto-Compare is a web based tool that permits comparison of commercial microarrays based on GO. Onto-Compare allows the user to assess the functional bias associated with each array and helps determine the best microarray for a given biological phenomenon described using GO terms. Onto-Compare is available from the Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
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Onto-Translate
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Onto-Translate is a web based tool that allows the user to quickly translate lists of accession IDs, UniGene cluster IDs and Affymetrix probe IDs from one to another. Onto-Translate helps identifying the same information across various databases and reduce the redundancy in arbitrary lists of genes. Onto-Translate is available from the Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
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Onto-Miner
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Onto-Miner allows searching of various public bioinformatics databases via clone ID, UniGene gene symbol, LocusLink ID, accession number etc. and can carry out batch mode queries using entire lists of genes. The site can be used as a resource by third party developers who would like to provide detailed gene information for arbitrary lists of genes. Onto-Miner is available from the Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
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GOblet
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The GOblet server running at the Max Planck Institute (MPI) for Molecular Genetics in Berlin performs analysis of sequences (cDNA, protein) with respect to GO terms. For similarity searches (BLAST), databases for various species are available, which were constructed using existing GO annotations. The server presents detailed descriptions of the matches and constructs a GO summary tree based on all GO terms of the respective hits.
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EASE
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EASE is a standalone software package from NIAID for use on Windows operating systems that is useful for summarizing the predominant biological "theme" of a given gene list. Given a list of genes resulting from a microarray or other genome-scale experiment, EASE can rapidly calculate over-representation statistics for every possible Gene Ontology term with respect to all genes represented in the data set.
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DAVID
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Database for Annotation, Visualization and Integrated Discovery (DAVID) is a web-based tool that provides integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.
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NetAffx Gene Ontology Mining Tool
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The NetAffx Gene Ontology Mining Tool from Affymetrix is free web tool for visualizing probe_sets based on GO annotations in the context of GO graphic structure (click on the GO analysis tab, registration is necessary). This tool is basically a GO-graph browser in the form of a heat map. It takes a input probe_set list, and GO nodes are colored based on the counts of hit, percentage of the sub-tree, or user specified parameters, allowing gene clusters to be identified visually.
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GARBAN
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GARBAN, from the University of Navarra, Spain, is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, SWISS-PROT, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications.
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FunSpec
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FunSpec is a web-based tool from the University of Toronto for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms. Help documentation is available online.
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GeneMerge
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GeneMerge, from Harvard University, returns functional genomic information for a given set of genes and provides statistical rank scores for over-representation of particular functions or categories in the dataset. All GO species are represented in addition to other species and functional genomic data.
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GoSurfer
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GoSurfer uses Gene Ontology information in the analysis of gene sets obtained from genome-wide computations, microarray analysis or any other highly parallel method. It includes rigorous statistical testing, interactive graphics and automated updating of the annotation available for common gene identifiers (UniGene, LocusLink) or Affymetrix probe sets. GoSurfer was written at the Harvard School of Public Health.
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CLENCH
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CLENCH (CLuster ENriCHment) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using Slimterm-lists (that can be edited by the user) and a local installation of GO. CLENCH was created at The Huck Institutes of the Life Sciences, Penn State.
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eGOn
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eGOn (explore Gene Ontology), developed at the Norwegian University of Science and Technology, is a web based tool for mapping microarray data onto the gene ontology structure. Several input files may be analyzed simultaneously to compare the distribution of the annotated genes for two or more experiments. Similarity/distance measures are introduced to enable identification of significant differences.
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More general tools
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Manatee
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Manatee is a web-based gene evaluation and genome annotation tool developed at TIGR. Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis.
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PubSearch
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PubSearch is a web-based literature curation tool developed at TAIR and available via GMOD. It allows curators to search and annotate genes to keywords from articles. It has a simple, mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. A demo is available.
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SOURCE
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SOURCE, developed by the Stanford Microarray Database (SMD) team, compiles information from several publicly accessible databases, including UniGene, dbEST, Swiss-Prot, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE.
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Onto-Express
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Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins. (Registration required; free for academics.)
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Genes2Diseases
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Genes2Diseases is a database of candidate genes for mapped inherited human diseases, developed by the Bork group at the European Molecular Biology Laboratory (EMBL). The database is generated using an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function (Gene Ontology) terms, based on the whole MEDLINE and RefSeq databases. Can be used to view all GO terms associated with a particular genetically inherited disease.
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GO Browsers
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Spotfire Gene Ontology Advantage Application
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The Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations.
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