Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher's Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies.
[Instance] id: TOOL:000002 type: tool name: g:Profiler url: http://biit.cs.ut.ee/gprofiler/ is_online_tool: true developer: ORG:000032 publication: PMID:17478515 license: free_academic description:g:Profiler is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology, pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are:
g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.
[Instance] id: TOOL:000003 type: tool name: GeneTools url: http://www.genetools.microarray.ntnu.no/common/intro.php is_online_tool: true developer: ORG:000061 developer: ORG:000049 license: free_academic description:GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology). The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO).
Major features are:
GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match.
[Instance] id: TOOL:000005 type: tool name: GoAnnotator url: http://xldb.fc.ul.pt/rebil/tools/goa/ is_online_tool: true developer: ORG:000017 publication: PMID:15719064 license: free_academic description:GoAnnotator is a tool for verification of electronic protein annotations using GO terms automatically extracted from literature.
[Instance] id: TOOL:000006 type: tool name: GOCat url: http://eagl.unige.ch/GOCat/ is_online_tool: true developer: ORG:000068 developer: ORG:000051 publication: PMID:16287934 publication: PMID:15960836 license: free_academic description:The Gene Ontology Categorizer (GOCat)[external website] is an automatic text categorizer. The tool classifies any input text (a few words, an abstract, a set of PubMed Identifiers...) into Gene Ontology categories. The system, originally developed for the first BioCreative evaluation campaign, aims at facilitating functional annotation of gene and gene products using text mining methods. For every predicted category, a confidence score and a short text passage, extracted from the input text, are provided. The interface can also be used to navigate the Gene Ontology thanks to direct Quick GO links.
[Instance] id: TOOL:000007 type: tool name: GoFigure url: http://udgenome.ags.udel.edu/gofigure/ is_online_tool: true developer: ORG:000028 publication: PMID:14668239 license: free_academic description:GoFigure is a web accessible tool that uses BLAST to predict Gene Ontology annotation by identifying annotated homologs of an unknown query sequence. Either DNA or protein sequences can be submitted, and multiple queries can be done by submitting a file containing FASTA formated sequences. Results are retrieved by email and may be viewed as either graphs or a tab delimited file. Results can also bedownloaded as a tar file.
[Instance] id: TOOL:000008 type: tool name: GoPubMed url: http://gopubmed.org/ is_online_tool: true developer: ORG:000059 publication: PMID:15980585 license: free_academic description:GoPubMed is a web server which allows users to explore PubMed search results with the Gene Ontology. GoPubMed submits a user's keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation.
[Instance] id: TOOL:000009 type: tool name: GOtcha url: http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html is_online_tool: true developer: ORG:000035 publication: PMID:15550167 license: free_academic description:GOtcha provides a prediction of a set of GO terms that can be assosciated with a given query sequence. Each term is scoredindependently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically.
The tool is currently web-based; contact David Martin for details of the standalone version.
High Throughput Gene Ontology Functional Annotation Toolkit allows for high throughput mapping of unknown or other genetic sequence data such as ESTs, mRNA, or protein data to Gene Ontology annotations, EC numbers and also directly to KEGG pathways. It uses sequence similarity and domain matching. The tool uses custom curated databases and has functions such as windows LAN distributed BLAST, which can distribute high throughput BLAST searches over a windows LAN. It has a high-throughput BLAST output viewer and many file type export features that allow for top hit association or manual curation of data. Data can be exported as AmiGO association files that can be loaded via the load data script. Pathways highlight those enzymes/genes that are represented in your dataset.
[Instance] id: TOOL:000011 type: tool name: InGOt url: http://www.biopendium.com/ingot.htm is_online_tool: true license: proprietary developer: ORG:000069 description:InGOt is a module for Inpharmatica's new modular system for protein annotation, a proprietary system for applying Gene Ontology to all proteins. It offers an unparalleled resource to elucidate protein function: its graphical user interface enables you to investigate links from summary data through to hierarchical context and literature/evidence links. InGOt has more sequences than any public resource and assignments harvested from the broadest possible GO-linked resources. InGOt can integrate with other modules such as Domain Professor for detailed protein domain annotation and Blu-Chip for instant and accurate probe to protein assignments.
[Instance] id: TOOL:000012 type: tool name: InterProScan url: http://www.ebi.ac.uk/Tools/InterProScan/ is_online_tool: true is_standalone_tool: true compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000086 publication: PMID:17202162 publication: PMID:15980438 license: free_academic description:Databases of protein domains and functional sites have become vital resources for the prediction of protein functions. During the last decade, several signature- recognition methods have evolved to address different sequence analysis problems, resulting in rather different and, for the most part, independent databases. Diagnostically, these resources have different areas of optimum application owing to the different strengths and weaknesses of their underlying analysis methods. Thus, for best results, search strategies should ideally combine all of them. InterProScan is a perl-based program which combines these different protein signature recognition methods into one resource.
[Instance] id: TOOL:000013 type: tool name: Joint Assembly of Functional Annotations synonym_acronym: JAFA url: http://jafa.burnham.org is_online_tool: true developer: ORG:000037 license: free_academic description:JAFA accepts a protein sequence, submits it to several function prediction programs, and provides an aggregate of the predictions in a single, easy to read display, based on GO terms. The user may click through to the individual servers, to AmiGO and QuickGO. JAFA also provides adownloadable XML file with the results, to enable incorporation in yet larger workflows.
[Instance] id: TOOL:000014 type: tool name: Manatee url: http://manatee.sourceforge.net/demos.shtml is_online_tool: true is_standalone_tool: true compatible_os: linux compatible_os: unix developer: ORG:000080 license: free_academic description:Manatee is a web-based gene evaluation and genome annotation tool; 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. Manatee can bedownloaded and installed to run under the CGI area of a web server, such as Apache.
[Instance] id: TOOL:000015 type: tool name: PubSearch url: http://pubsearch.org is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000062 license: free_academic description:PubSearch is a web-based literature curation tool, allowing 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 using data from TAIR is available (runs on platforms supporting Java Servlets environment); the tool itself can bedownloaded from GMOD.
[Instance] id: TOOL:000016 type: tool name: AmiGO url: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi email: gohelp@geneontology.org is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000009 feature: ont_view feature: annot_view license: free_academic description:AmiGO provides an interface to search and browse the ontology and annotation data provided by the GO consortium. Users can search for gene products and view the terms with which they are associated; alternatively, users can search or browse the ontology for GO terms of interest and see term details and gene product annotations. AmiGO also provides a BLAST search engine, which searches the sequences of genes and gene products that have been annotated to a GO term and submitted to the GO Consortium.
AmiGO accesses the GO mySQL database; more information is available from the GO database guide.
[Instance] id: TOOL:000017 type: tool name: GO Online SQL Environment acronym: GOOSE url: http://www.berkeleybop.org/goose/ email: gohelp@geneontology.org is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000009 feature: godb feature: annot_view license: free_academic description:GOOSE, the GO Online SQL Environment, provides a direct interface to the GO database, allowing users to run custom queries without having to install a copy of the GO database locally.
[Instance] id: TOOL:000018 type: tool name: CGAP GO Browser url: http://cgap.nci.nih.gov/Genes/GOBrowser is_online_tool: true developer: ORG:000053 license: free_academic description:With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term.
GO data updated every few months.
COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL.
[Instance] id: TOOL:000020 type: tool name: Comparative Toxicogenomics Database synonym_acronym: CTD url: http://ctd.mdibl.org/ is_online_tool: true developer: ORG:000022 publication: PMID:16902965 publication: PMID:16675512 publication: PMID:14735110 publication: PMID:12760826 license: free_academic description:The Comparative Toxicogenomics Database (CTD) is a public database that enhances understanding about the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures.
[Instance] id: TOOL:000021 type: tool name: DynGO url: http://gauss.dbb.georgetown.edu/liblab/dyngo.html is_standalone_tool: true compatible_os: win compatible_os: unix compatible_os: linux developer: ORG:000083 publication: PMID:16091147 license: free_academic description:DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples.
[Instance] id: TOOL:000022 type: tool name: EP GO Browser url: http://ep.ebi.ac.uk/EP/GO/ is_online_tool: true developer: ORG:000086 license: free_academic description: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.
[Instance] id: TOOL:000023 type: tool name: Gene Class Expression url: http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl is_online_tool: true developer: ORG:000075 publication: PMID:16755502 license: free_academic description:Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing.
[Instance] id: TOOL:000024 type: tool name: GeneInfoViz url: http://genenet2.utmem.edu/geneinfoviz is_online_tool: true developer: ORG:000082 publication: PMID:15724283 license: free_academic description:GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG.
[Instance] id: TOOL:000025 type: tool name: GeneOntology at RZPD url: http://www.rzpd.de/cgi-bin/asearch/GO/go4rzpd.pl.cgi is_online_tool: true developer: ORG:000045 license: free_academic description:With the RZPD GeneOntology tool, 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.
! not sure what's happening with this tool - may no longer be active. [Instance] id: TOOL:000026 type: tool name: GenNav url: http://mor.nlm.nih.gov/perl/gennav.pl is_online_tool: true developer: ORG:000078 license: free_academic description:GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.
[Instance] id: TOOL:000027 type: tool name: GOblet url: http://goblet.molgen.mpg.de/ is_online_tool: true developer: ORG:000008 publication: PMID:15215401 license: free_academic description:The GOblet server 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.
[Instance] id: TOOL:000028 type: tool name: GoFish url: http://llama.med.harvard.edu/~berriz/GoFishWelcome.html is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000014 publication: PMID:12691998 license: free_academic description:The GoFish program, available as a Java applet online or todownload, 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.
[Instance] id: TOOL:000029 type: tool name: GONUTS url: http://gowiki.tamu.edu/ is_online_tool: true developer: ORG:000088 license: free_academic description:GONUTS (Gene Ontology Normal Usage Tracking System) is a wiki based browser for GO terms and gene associations for a limited set of organisms. The wiki interface allows users to record and share notes about the usage of each GO term.
[Instance] id: TOOL:000030 type: tool name: MGI GO Browser url: http://www.informatics.jax.org/searches/GO_form.shtml is_online_tool: true developer: ORG:000006 license: free_academic description: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 data in the MGI database, which is updated nightly.
[Instance] id: TOOL:000031 type: tool name: OBO-Edit url: https://sourceforge.net/project/showfiles.php?group_id=36855&package_id=192411 email: gohelp@geneontology.org is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000009 license: free_academic description:OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.
OBO-Edit uses the OBO format flat file.
[Instance] id: TOOL:000032 type: tool name: Ontology Lookup Service url: http://www.ebi.ac.uk/ontology-lookup/ is_online_tool: true developer: ORG:000086 publication: PMID:16507094 license: free_academic description:The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available fordownload from SourceForge. All OLS source code is publicly available under the open source Apache Licence. The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format.
[Instance] id: TOOL:000033 type: tool name: PANDORA url: http://www.pandora.cs.huji.ac.il is_online_tool: true developer: ORG:000063 license: free_academic description:With PANDORA, 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 UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group.
[Instance] id: TOOL:000034 type: tool name: QuickGO at EBI url: http://www.ebi.ac.uk/ego/ is_online_tool: true developer: ORG:000086 license: free_academic description: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. The GO data is updated daily.
[Instance] id: TOOL:000035 type: tool name: TAIR Keyword Browser url: http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword is_online_tool: true developer: ORG:000062 license: free_academic description:TAIR Keyword Browser 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.
[Instance] id: TOOL:000036 type: tool name: Tk-GO url: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-gui/?cvsroot=bioperl is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000070 license: free_academic description:This tool is a GUI wrapping the basic functions of the GO::AppHandle library from BDGP. 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 todownload the programme. All available documentation is included in thisdownload. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable.
[Instance] id: TOOL:000037 type: tool name: Agile Protein Interaction Data Analyzer url: http://bioinfow.dep.usal.es/apid/index.htm is_online_tool: true developer: ORG:000046 publication: PMID:16845013 license: free_academic description:Agile Protein Interaction Data Analyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore more than 40000 different proteins and close to 150000 different proven interactions. The website includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Parameters for the proteins are connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; for the interactions: number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network.
[Instance] id: TOOL:000038 type: tool name: Db for Dummies! url: http://www.dbfordummies.com/go.asp is_standalone_tool: true compatible_os: win developer: ORG:000040 license: free_academic description:Db for Dummies! (DBD) is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree.
[Instance] id: TOOL:000039 type: tool name: Flash GViewer url: http://www.gmod.org/wiki/index.php/Flashgviewer/ is_online_tool: true developer: ORG:000026 license: free_academic description:Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes associated with a specific ontology term, etc., rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts.
This tool is not GO-specific, but was built for the purpose of viewing GO annotation data.
FunSpec is a web-based tool 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.
[Instance] id: TOOL:000041 type: tool name: Generic GO Term Mapper url: http://go.princeton.edu/cgi-bin/GOTermMapper is_online_tool: true developer: ORG:000081 license: free_academic description:The Generic GO Term Mapper is a tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms (sometimes referred to as GO Slim terms), allowing you to bin your genes into broad categories.
[Instance] id: TOOL:000042 type: tool name: Genes2Diseases url: http://www.bork.embl-heidelberg.de/g2d/ is_online_tool: true developer: ORG:000084 license: free_academic description:Genes2Diseases is a database of candidate genes for mapped inherited human diseases. The database is generated using an analysis of relations between phenotypic features and chemical objects, and from chemical objects to Gene Ontology protein function terms, based on the whole MEDLINE and RefSeq databases. Can be used to view all GO terms associated with a particular genetically inherited disease.
[Instance] id: TOOL:000043 type: tool name: GO Slim Mapper url: http://db.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl is_online_tool: true developer: ORG:000025 license: free_academic description:The GO Slim Mapper (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms. Uses the SGD GO Slim sets.
[Instance] id: TOOL:000044 type: tool name: GO Terms Classifications Counter url: http://www.animalgenome.org/bioinfo/tools/countgo/ is_online_tool: true developer: ORG:000002 license: free_academic description:GO Terms Classifications Counter takes input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim or GO-ROOT, performs the count, and returns the results on the web (if it takes too long, it will email the user with the results link). The results include a sorted table of counts, percentages, and a pie chart.
[Instance] id: TOOL:000045 type: tool name: Gene Ontology Browsing Utility synonym_acronym: GOBU url: http://gobu.iis.sinica.edu.tw/ is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000055 license: free_academic description:Gene Ontology Browsing Utility (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable architecture that uses the Gene Ontology and a user-defined hierarchy as two main atalogs. GOBU has the following features: (1) user-specified hierarchical data as input data, (2) user-defined data types for describing different annotations, and (3) an extendable software architecture for handling user-defined data types.
[Instance] id: TOOL:000046 type: tool name: GOChase url: http://www.snubi.org/software/GOChase/ is_online_tool: true developer: ORG:000047 publication: PMID:15513987 license: free_academic description:GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.
GOProfiler provides a summary of the GO annotations available in AgBase. The user provides a species (taxon id) and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.
[Instance] id: TOOL:000048 type: tool name: GORetriever url: http://agbase.msstate.edu/GORetriever.html is_online_tool: true developer: ORG:000044 license: free_academic description:GORetriever is used to find all of the GO annotations in AgBase corresponding to a list of user-supplied protein identifiers. Currently supported ID types are Uniprot ID, Uniprot Accession, and GO ID. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. The list without GO annotations can be subsequently used as in put for the GOanna tool that finds similar sequences with annotations (where they are available).
[Instance] id: TOOL:000049 type: tool name: GOSlimViewer url: http://agbase.msstate.edu/GOSlimViewer.html is_online_tool: true developer: ORG:000044 license: free_academic description:GOSlimViewer is used to provide a high level summary of the GO categories for a dataset. It is designed to use output generated by GORetriever. Note that you can add additional annotations that come from GOanna (or other sources) to the GORetriever file. GOSlimViewer currently only supports the listed GOSlim sets.
[Instance] id: TOOL:000050 type: tool name: ProteInOn url: http://xldb.fc.ul.pt/biotools/proteinon/ is_online_tool: true developer: ORG:000017 publication: PMID:15960834 license: free_academic description:ProteInOn can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of proteins and to get the information content and calculate the functional semantic similarity of GO terms.
Additional citations:
TXTGate is a web-service that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles.
[Instance] id: TOOL:000052 type: tool name: Wandora url: http://www.wandora.org is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000071 license: free_academic description:Wandora is a general purpose knowledge extraction, management, and publishing environment based on Topic Maps (ISO 13250). Wandora supports OBO flat file v1.2 format and can convert OBO files, including the Gene Ontology, to a topic map and vice versa. Wandora is well suited to OBO visualizations and knowledge mashups combining OBO, RDF(S), and Topic Map resources for example.
Wandora requires Java v6.
[Instance] id: TOOL:000053 type: tool name: WEGO url: http://wego.genomics.org.cn is_online_tool: true developer: ORG:000072 license: free_academic description:WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks.
[Instance] id: TOOL:000054 type: tool name: Whatizit url: http://www.ebi.ac.uk/Rebholz-srv/whatizit/form.jsp is_online_tool: true developer: ORG:000042 license: free_academic description:Whatizit is a web application which highlights all kinds of "interesting" things in a document. One of its modules marks all GO terms as well as protein and gene names from UniProt and links them to their entries in GO and UniProt respectively.
[Instance] id: TOOL:000055 type: tool name: Avadis url: http://avadis.strandgenomics.com is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: linux license: proprietary developer: ORG:000021 description:Avadis is a data analysis and visualization tool for gene expression data. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Genes can be clustered based on ontology terms to identify functional signatures in gene expression clusters.
[Instance] id: TOOL:000056 type: tool name: BiNGO url: http://www.psb.ugent.be/cbd/papers/BiNGO/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000029 publication: PMID:15972284 license: free_academic description:BiNGO is an open-source Java tool to determine which GO categories are statistically over-represented in a set of genes. BiNGO is implemented as a plugin for Cytoscape, which is a software platform for data integration and visualization of molecular interaction networks. BiNGO maps the predominant functional themes of a given gene set on the GO hierarchy, and outputs this mapping as a Cytoscape graph.
[Instance] id: TOOL:000057 type: tool name: CLENCH url: http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench is_standalone_tool: true compatible_os: win compatible_os: linux developer: ORG:000004 publication: PMID:14764555 license: free_academic description: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 GO slim term lists (which can be edited by the user) and a local installation of GO.
[Instance] id: TOOL:000058 type: tool name: DAVID url: http://david.abcc.ncifcrf.gov/ is_online_tool: true developer: ORG:000050 publication: PMID:12734009 license: free_academic description: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.
[Instance] id: TOOL:000059 type: tool name: EASE url: http://david.niaid.nih.gov/david/ease.htm is_standalone_tool: true compatible_os: win developer: ORG:000050 publication: PMID:12734009 license: free_academic description:EASE 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.
[Instance] id: TOOL:000060 type: tool name: eGOn v2.0 url: http://www.genetools.microarray.ntnu.no/common/intro.php is_online_tool: true developer: ORG:000061 developer: ORG:000049 license: free_academic description:eGOn V2.0 (explore Gene Ontology) is a web-based tool for mapping microarray data on to the Gene Ontology structure. Several input files may be analyzed simultaneously to compare the distribution of the annotated genes for two or more experiments.
Essential features of eGOn V2.0 are:
ermineJ is a tool for the analysis of gene sets (user defined or those defined by GO terms) in expression data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Several different methods for scoring gene sets are implemented, with a focus on methods that don't rely on simple "over-representation" measures.
[Instance] id: TOOL:000062 type: tool name: FatiGO url: http://fatigo.ochoa.fib.es is_online_tool: true developer: ORG:000064 publication: PMID:14990455 license: free_academic description:FatiGO 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 Gene Expression Pattern Analysis Suite. FatiGO uses gene IDs from the major genomic and proteomic databases (GeneBank, UniProt, Unigene, Ensembl, etc.). FatiGO can also be used for functional annotation of any type of large-scale experiment.
[Instance] id: TOOL:000063 type: tool name: Functional Information Viewer and Analyzer synonym_acronym: FIVA url: http://bioinformatics.biol.rug.nl/standalone/fiva/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000056 publication: PMID:17237043 license: free_academic description:FIVA aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes.
[Instance] id: TOOL:000064 type: tool name: FuncAssociate url: http://llama.med.harvard.edu/cgi/func/funcassociate is_online_tool: true developer: ORG:000014 publication: PMID:14668247 license: free_academic description:FuncAssociate is a web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 10 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff.
A new version of FuncAssociate (still at the beta stage!) is now available. This version supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented.
[Instance] id: TOOL:000065 type: tool name: FuncExpression url: http://www.barleybase.org/funcexpression.php is_online_tool: true developer: ORG:000007 license: free_academic description:FuncExpression is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase.
[Instance] id: TOOL:000066 type: tool name: Functional Profiling of Microarray Expression Data synonym_abbr: FunCluster url: http://corneliu.henegar.info/FunCluster.htm is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000018 publication: PMID:17007070 publication: PMID:16506959 publication: PMID:16046292 license: free_academic description:FunCluster is a genomic data analysis tool designed to perform a functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis allows to detect co-regulated biological processes (i.e. represented by annotating genomic themes) through a specifically designed co-clustering procedure involving biological annotations and gene expression data. FunCluster's functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo sapiens, Mus musculus and Saccharomyces cerevisiae.
FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix).download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0.
[Instance] id: TOOL:000067 type: tool name: Functional Analysis of Transcriptional Networks synonym_abbr: FunNet url: http://www.funnet.info is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000018 publication: PMID:18208606 license: free_academic description:FunNet is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes.
FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can bedownloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0.
[Instance] id: TOOL:000068 type: tool name: G-SESAME url: http://bioinformatics.clemson.edu/G-SESAME/ is_online_tool: true developer: ORG:000024 publication: PMID:17344234 license: free_academic description:G-SESAME contains a set of tools. They are
GARBAN 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, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban@ceit.es.
[Instance] id: TOOL:000070 type: tool name: GENECODIS url: http://genecodis.dacya.ucm.es/ is_online_tool: true developer: ORG:000019 developer: ORG:000085 publication: PMID:17204154 license: free_academic description:GENECODIS is a web-based tool for the functional analysis of gene lists. It integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by their statistical significance. It allows the analysis of annotations from different databases such as GO, KEGG or SwissProt.
[Instance] id: TOOL:000071 type: tool name: GeneMerge url: http://genemerge.cbcb.umd.edu/ is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000036 publication: PMID:12724301 license: free_academic description:GeneMerge 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.
[Instance] id: TOOL:000072 type: tool name: Genome Function INtegrated Discoverer synonym_abbr: GFINDer url: http://www.medinfopoli.polimi.it/GFINDer/ is_online_tool: true developer: ORG:000077 license: free_academic description:GFINDer: Genome Function INtegrated Discoverer is a multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyse the obtained classifications, aiding in better interpreting microarray experiment results.
[Instance] id: TOOL:000073 type: tool name: Generalized Ontological Algorithmic Logical Invariants Extractor synonym_abbr: GOALIE url: http://bioinformatics.nyu.edu/Projects/GOALIE/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: linux developer: ORG:000003 license: free_academic description:GOALIE (Generalized Ontological Algorithmic Logical Invariants Extractor) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database.
[Instance] id: TOOL:000074 type: tool name: GOdist url: http://basalganglia.huji.ac.il/links.htm is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000063 publication: PMID:15550480 license: free_academic description:GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component).
[Instance] id: TOOL:000075 type: tool name: GOHyperGAll url: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#go is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000015 license: free_academic description:To test a sample population of genes for overrepresentation of GO terms, the R/BioC function GOHyperGAll computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool.
[Instance] id: TOOL:000076 type: tool name: High-Throughput GoMiner and MatchMiner url: http://discover.nci.nih.gov/gominer/htgm.jsp is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000039 developer: ORG:000052 publication: PMID:14728344 license: free_academic description:High-Throughput GoMiner is an 'industrial-strength' integrative Gene Ontology tool for interpretation of multiple-microarray experiments. 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. For users running under a Unix-based operating system, there is an automated script for easy installation of the local database.
[Instance] id: TOOL:000077 type: tool name: GOstat url: http://gostat.wehi.edu.au is_online_tool: true developer: ORG:000011 publication: PMID:14962934 license: free_academic description:GOstat, is an easy to use web tool to determine statistically significant over- or under-represented GO categories within lists of genes. Data files are updating monthly.
[Instance] id: TOOL:000078 type: tool name: GoSurfer url: http://biosun1.harvard.edu/complab/gosurfer/ is_standalone_tool: true compatible_os: win developer: ORG:000038 license: free_academic description: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.
See also the GO Surfer paper (PDF format).
[Instance] id: TOOL:000079 type: tool name: GO Term Finder url: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.pl is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000025 publication: PMID:15297299 license: free_academic description: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 Saccharomyces Genome Database searches annotations of budding yeast gene products. A generic GO Term Finder has been created by Stanford Microarray Database and can bedownloaded from CPAN. This code has been used to implement a web-based generic GO Term Finder by the Princeton genomics group; this implementation provides analysis, via a web tool, of genes from any species (including human) for which there are GO annotations publicly available through the GO web site.
[Instance] id: TOOL:000080 type: tool name: Gene Ontology Tree Machine synonym_acronym: GOTM url: http://bioinfo.vanderbilt.edu/gotm/ is_online_tool: true developer: ORG:000074 developer: ORG:000057 publication: PMID:14975175 license: free_academic description:GOTM is a web-based tool for the analysis and visualization of sets of interesting genes based on Gene Ontology hierarchies. This tool provides user friendly data navigation and visualization. It generates expandable tree for browsing the GO hierarchy, fixed tree as HTML output for archive and Bar charts at different annotation levels for publication. GOTM provides statistical analysis to indicate GO categories with relatively enriched gene numbers and suggest biological areas that warrant further study. Enriched GO categories can be visualized in Sub-trees or DAGs. Subset of genes can be retrieved by GO term or keyword searching. Detailed information for each gene can be retrieved directly from our a local database GeneKeyDB.
[Instance] id: TOOL:000081 type: tool name: GOToolBox url: http://gin.univ-mrs.fr/GOToolBox/ is_online_tool: true developer: ORG:000048 publication: PMID:15575967 license: free_academic description:GOToolBox is a series of web-based programs allowing the identification of statistically over- or under-represented terms in a gene dataset relative to a reference gene set; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology and terms can be filtered on evidence codes. Updated monthly with GO and gene association files.
[Instance] id: TOOL:000082 type: tool name: L2L url: http://depts.washington.edu/l2l/ is_online_tool: true is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000073 publication: PMID:16168088 license: free_academic description:L2L is a simple but powerful tool for discovering the hidden biological significance in microarray data. Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. Adownloadable command-line version can run customized and batch analyses.
[Instance] id: TOOL:000083 type: tool name: MAPPFinder url: http://www.genmapp.org/ is_standalone_tool: true compatible_os: win developer: ORG:000034 publication: PMID:12540299 license: free_academic description: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.
[Instance] id: TOOL:000084 type: tool name: Onto-Compare url: http://vortex.cs.wayne.edu/projects.htm#Onto-Compare is_online_tool: true developer: ORG:000031 publication: PMID:12664686 publication: PMID:15215428 license: free_academic description: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.
[Instance] id: TOOL:000085 type: tool name: Onto-Design url: http://vortex.cs.wayne.edu/projects.htm#Onto-Design is_online_tool: true developer: ORG:000031 publication: PMID:15215428 license: free_academic description: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.
[Instance] id: TOOL:000086 type: tool name: Onto-Express url: http://vortex.cs.wayne.edu/projects.htm#Onto-Express is_online_tool: true developer: ORG:000031 publication: PMID:11829497 publication: PMID:12620386 publication: PMID:15215428 license: free_academic description: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.
[Instance] id: TOOL:000087 type: tool name: Onto-Miner url: http://vortex.cs.wayne.edu/projects.htm#Onto-Miner is_online_tool: true developer: ORG:000031 publication: PMID:15215428 license: free_academic description: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.
[Instance] id: TOOL:000088 type: tool name: Onto-Translate url: http://vortex.cs.wayne.edu/projects.htm#Onto-Translate is_online_tool: true developer: ORG:000031 publication: PMID:15215428 license: free_academic description: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.
[Instance] id: TOOL:000089 type: tool name: OntoGate url: http://functionalgenomics.de/ontogate/ is_online_tool: true developer: ORG:000008 publication: PMID:12824422 license: free_academic description: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.
[Instance] id: TOOL:000090 type: tool name: Ontologizer url: http://www.charite.de/ch/medgen/ontologizer/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000023 publication: PMID:14764576 license: free_academic description:Ontologizer can be used to generate listings of GO annotations for one or many groups of genes/gene products. GO annotations, ranked according to frequency for each cluster, are displayed in HTML or XML format. If a population dataset is provided, statistical analysis for overrepresentation of individual GO terms is performed. "Dot" (GraphViz) files can be generated to provide a graphical overview of overrepresented GO terms in the GO graph structure. Detailed listings for each gene are also provided.
[Instance] id: TOOL:000091 type: tool name: Ontology Traverser url: http://franklin.imgen.bcm.tmc.edu/rho/services/index.jsp?page=OntologyTraverser is_online_tool: true developer: ORG:000066 publication: PMID:15333457 license: free_academic description:OntologyTraverser is a microarray gene list enrichment tool. Our tool provides an easy upload format accepting AffyIDs or NIAIDs for some cDNA chips and comparison of the lists against the entire probe/clone collection for the array type used. We support several report formats: flat html, flat tsv, xml and a dynamic/clickable HTML which displays the GO structure. A variety of statistics/results are reported for each GO node: the list fq, array fq, fold change, a Fisher's exact test p-value and the identities of the genes mapped at or below each node.
[Instance] id: TOOL:000092 type: tool name: Probe Explorer url: http://probeexplorer.cicancer.org/ is_online_tool: true developer: ORG:000001 country-name: Spain license: free_academic description:Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query.
[Instance] id: TOOL:000093 type: tool name: Profiling of Complex Functionality synonym_abbr: ProfCom url: http://webclu.bio.wzw.tum.de/profcom/ is_online_tool: true developer: ORG:000065 publication: PMID:16959266 license: free_academic description:ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes.
[Instance] id: TOOL:000094 type: tool name: SeqExpress url: http://www.seqexpress.com/ is_standalone_tool: true compatible_os: win developer: ORG:000010 publication: PMID:14988116 license: free_academic description:SeqExpress is a comprehensive analysis and visualisation package for gene expression experiments. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualisation, file export/import, searching, integration (with R), and clustering options.
[Instance] id: TOOL:000095 type: tool name: SerbGO url: http://estbioinfo.stat.ub.es/apli/serbgo/ is_online_tool: true developer: ORG:000043 license: free_academic description:SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one.
[Instance] id: TOOL:000096 type: tool name: SOURCE url: http://source.stanford.edu/ is_online_tool: true developer: ORG:000060 publication: PMID:12519986 license: free_academic description:SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE.
[Instance] id: TOOL:000097 type: tool name: Spotfire Gene Ontology Advantage Application url: http://www.spotfire.com/services/advantage.asp is_standalone_tool: true compatible_os: win developer: ORG:000012 license: proprietary description: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.
[Instance] id: TOOL:000098 type: tool name: Short Time-series Expression Miner synonym_acronym: STEM url: http://www.cs.cmu.edu/~jernst/stem/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000030 publication: PMID:15961453 publication: PMID:16597342 license: free_academic description:The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data (8 time points or less). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database and supports GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category, identifying which temporal expression profiles were enriched for these genes.
[Instance] id: TOOL:000099 type: tool name: T-Profiler url: http://www.t-profiler.org/ is_online_tool: true developer: ORG:000076 developer: ORG:000087 publication: PMID:15980543 license: free_academic description:T-Profiler uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters.
[Instance] id: TOOL:000100 type: tool name: THEA url: http://bioinfo.unice.fr is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000059 publication: PMID:15130932 license: free_academic description:THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining).
[Instance] id: TOOL:000101 type: tool name: FuSSiMeG url: http://xldb.fc.ul.pt/biotools/rebil/ssm/ is_online_tool: true developer: ORG:000005 license: free_academic description:With FuSSiMeG (Functional Semantic Similarity Measure between Gene Products), you can measure the functional similarity between gene products, by comparing the semantic similarity between the GO terms in their annotations. You can also measure the semantic similarity between any GO terms.
[Instance] name: GOArray url: http://ycmi.med.yale.edu/gomine/ is_standalone_tool: true compatible_os: win compatible_os: mac compatible_os: unix compatible_os: linux developer: ORG:000041 license: free_academic description:GOArray is a Perl program which inputs a lists of genes annotated as "of interest" (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used.
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[Instance] id: ORG:000001 type: developer name: Centro de Investigacion del Cancer organization-name: University of Salamanca url: http://www.cicancer.org locality: Salamanca country-name: Spain [Instance] id: ORG:000002 type: developer name: U.S. National Animal Genome Research Program (NAGRP) url: http://www.animalgenome.org [Instance] id: ORG:000003 type: developer name: NYU Bioinformatics Group url: http://bioinformatics.nyu.edu [Instance] id: ORG:000004 type: developer name: Huck Institutes of the Life Sciences organization-name: Penn State url: http://www.hils.psu.edu region: Pennsylvania country-name: USA [Instance] id: ORG:000005 type: developer name: University of Lisbon url: http://www.ul.pt country-name: Portugal [Instance] id: ORG:000006 type: developer name: Mouse Genome Informatics url: http://www.informatics.jax.org [Instance] id: ORG:000007 type: developer name: Iowa State University url: http://www.iastate.edu [Instance] id: ORG:000008 type: developer name: Max Planck Institute for Molecular Genetics url: http://www.molgen.mpg.de locality: Berlin country-name: Germany [Instance] id: ORG:000009 type: developer name: The Gene Ontology Consortium url: http://www.geneontology.org [Instance] id: ORG:000010 type: developer name: SeqExpress url: http://www.seqexpress.com [Instance] id: ORG:000011 type: developer name: Walter and Eliza Hall Institute of Medical Research url: http://www.wehi.edu.au locality: Melbourne country-name: Australia [Instance] id: ORG:000012 type: developer name: Spotfire, Inc. url: http://www.spotfire.com [Instance] id: ORG:000013 type: developer name: Bioengineering, Electronics and Telemedicine Group organization-name: ITACA, Universidad Politécnica de Valencia url: http://www.bet.upv.es locality: Valencia country-name: Spain [Instance] id: ORG:000014 type: developer name: Roth lab organization-name: Harvard Medical School url: http://llama.med.harvard.edu [Instance] id: ORG:000015 type: developer name: University of California, Riverside url: http://www.ucr.edu [Instance] id: ORG:000016 type: developer name: Centro de Genómica organization-name: Instituto Valenciano de Investigaciones Agrarias url: http://www.ivia.es/centrogenomica/inicioconmarco.htm locality: Valencia country-name: Spain [Instance] id: ORG:000017 type: developer name: XLDB Group organization-name: Faculty of Sciences at the University of Lisbon url: http://xldb.fc.ul.pt locality: Lisbon country-name: Portugal [Instance] id: ORG:000018 type: developer name: Institut National de la Santé et de la Recherche Medicale synonym_acronym: INSERM organization-name: Centre de Recherche des Cordeliers url: http://www.inserm.fr/en/ locality: Paris country-name: France [Instance] id: ORG:000019 type: developer name: National Center of Biotechnology (CNB-CSIC) url: http://www.cnb.csic.es locality: Madrid country-name: Spain [Instance] id: ORG:000020 type: developer name: University of Toronto url: http://www.utoronto.ca/bandb country-name: Canada [Instance] id: ORG:000021 type: developer name: Strand Genomics url: http://www.strandgenomics.com [Instance] id: ORG:000022 type: developer name: Mount Desert Island Biological Laboratory url: http://www.mdibl.org region: Maine country-name: USA [Instance] id: ORG:000023 type: developer name: Charité University Hospital url: http://www.charite.de/ch/medgen/ country-name: Germany [Instance] id: ORG:000024 type: developer name: Clemson Bioinformatics Center url: http://bioinformatics.clemson.edu region: South Carolina country-name: USA [Instance] id: ORG:000025 type: developer name: Saccharomyces Genome Database url: http://www.yeastgenome.org [Instance] id: ORG:000026 type: developer name: Twigger Lab organization-name: Medical College of Wisconsin url: http://www.phys.mcw.edu/fac_twigger.htm [Instance] id: ORG:000027 type: developer name: Center for Computational Biology and Bioinformatics organization-name: Columbia University url: http://www.c2b2.columbia.edu [Instance] id: ORG:000028 type: developer name: University of Delaware url: http://www.udel.edu [Instance] id: ORG:000029 type: developer name: Department of Plant Systems Biology organization-name: VIB / Ghent University url: http://www.psb.ugent.be [Instance] id: ORG:000030 type: developer name: Carnegie Mellon University url: http://www.cmu.edu [Instance] id: ORG:000031 type: developer name: Intelligent Systems and Bioinformatics Laboratory organization-name: Wayne State University url: http://vortex.cs.wayne.edu [Instance] id: ORG:000032 type: developer name: University of Tartu url: http://www.ut.ee country-name: Estonia [Instance] id: ORG:000033 type: developer name: University of Navarra url: http://www.unav.es country-name: Spain [Instance] id: ORG:000034 type: developer name: Gladstone Institutes organization-name: University of California url: http://www.gladstone.ucsf.edu [Instance] id: ORG:000035 type: developer name: Barton group organization-name: University of Dundee url: http://www.compbio.dundee.ac.uk [Instance] id: ORG:000036 type: developer name: Harvard University url: http://www.oeb.harvard.edu [Instance] id: ORG:000037 type: developer name: Burnham Institute for Medical Research url: http://www.burnham.org country-name: USA [Instance] id: ORG:000038 type: developer name: Harvard School of Public Health url: http://www.hsph.harvard.edu [Instance] id: ORG:000039 type: developer name: Genomics and Bioinformatics Group of LMP, NCI, NIH url: http://discover.nci.nih.gov [Instance] id: ORG:000040 type: developer name: Custom Microsystems url: http://www.dbfordummies.com/ContactInfo.asp [Instance] id: ORG:000041 type: developer name: Yale Center for Medical Informatics url: http://ycmi.med.yale.edu [Instance] id: ORG:000042 type: developer name: Rebholz group organization-name: European Bioinformatics Institute url: http://www.ebi.ac.uk/Rebholz/ [Instance] id: ORG:000043 type: developer name: Statistics and Bioinformatics Research Group organization-name: University of Barcelona url: http://estbioinfo.stat.ub.es/estbioinfo/index.htm [Instance] id: ORG:000044 type: developer name: AgBase url: http://www.agbase.msstate.edu [Instance] id: ORG:000045 type: developer name: RZPD Deutsches Ressourcenzentrum für Genomforschung url: http://www.rzpd.de [Instance] id: ORG:000046 type: developer name: Bioinformatics and Functional Genomics Research Group synonym_acronym: CiC, CSIC-USAL organization-name: Cancer Research Center url: http://bioinfow.dep.usal.es locality: Salamanca country-name: Spain [Instance] id: ORG:000047 type: developer name: Seoul National University Biomedical Informatics url: http://www.snubi.org [Instance] id: ORG:000048 type: developer name: Developmental Biology Institute of Marseille url: http://www.ibdm.univ-mrs.fr country-name: France [Instance] id: ORG:000049 type: developer name: Norwegian Microarray Consortium url: http://www.microarray.no [Instance] id: ORG:000050 type: developer name: National Institute of Allergy and Infectious Diseases url: http://www.niaid.nih.gov [Instance] id: ORG:000051 type: developer name: Swiss-Prot group organization-name: Swiss Institute of Bioinformatics url: http://www.isb-sib.ch/groups/Swiss-Prot.htm [Instance] id: ORG:000052 type: developer name: Medical Informatics and Bioimaging group organization-name: BME, Georgia Tech/Emory University url: http://www.miblab.gatech.edu [Instance] id: ORG:000053 type: developer name: Cancer Genome Anatomy Project url: http://cgap.nci.nih.gov [Instance] id: ORG:000054 type: developer name: XSPAN project organization-name: University of Edinburgh url: http://www.xspan.org country-name: UK [Instance] id: ORG:000055 type: developer name: Institute of Information Science organization-name: Academia Sinica url: http://www.iis.sinica.edu.tw/index.htm country-name: Taiwan [Instance] id: ORG:000056 type: developer name: Groningen Biomolecular Sciences and Biotechnology Institute url: http://molgen.biol.rug.nl/molgen/index.php locality: Haren country-name: the Netherlands [Instance] id: ORG:000057 type: developer name: Oak Ridge National Laboratory (ORNL) url: http://gst.ornl.gov [Instance] id: ORG:000058 type: developer name: Virtual Biology Lab organization-name: Institute of Signaling, Developmental Biology and Cancer Research url: http://bioinfo.unice.fr country-name: France [Instance] id: ORG:000059 type: developer name: Biotechnological Centre organization-name: Technological University, Dresden url: http://www.biotec.tu-dresden.de locality: Dresden country-name: Germany [Instance] id: ORG:000060 type: developer name: Stanford Microarray Database url: http://genome-www5.stanford.edu [Instance] id: ORG:000061 type: developer name: Norwegian University of Science and Technology url: http://www.ntnu.no locality: Trondheim country-name: Norway [Instance] id: ORG:000062 type: developer name: The Arabidopsis Information Resource url: http://www.arabidopsis.org [Instance] id: ORG:000063 type: developer name: The Hebrew University of Jerusalem url: http://www.huji.ac.il/huji/eng/index_e.htm country-name: Israel [Instance] id: ORG:000064 type: developer name: Bioinformatics Department organization-name: Centro de Investigacion Principe Felipe url: http://bioinfo.ochoa.fib.es locality: Valencia country-name: Spain [Instance] id: ORG:000065 type: developer name: The Institute of Bioinformatics and Systems Biology organization-name: Helmholtz Zentrum München url: http://mips.gsf.de locality: Munich country-name: Germany [Instance] id: ORG:000066 type: developer name: Baylor College of Medicine url: http://franklin.imgen.bcm.tmc.edu [Instance] id: ORG:000067 type: developer name: Bioinformatics group organization-name: ESAT / K. U. Leuven url: http://www.kuleuven.be/bioinformatics/ country-name: Belgium [Instance] id: ORG:000068 type: developer name: Text Mining group organization-name: University of Geneva url: http://www.natlang.hcuge.ch country-name: Switzerland [Instance] id: ORG:000069 type: developer name: Inpharmatica url: http://www.inpharmatica.co.uk [Instance] id: ORG:000070 type: developer name: Illuminae url: http://www.illuminae.com [Instance] id: ORG:000071 type: developer name: Grip Studios Interactive, Inc. url: http://www.gripstudios.com [Instance] id: ORG:000072 type: developer name: Beijing Genomics Institute url: http://www.genomics.org.cn country-name: China [Instance] id: ORG:000073 type: developer name: Department of Biochemistry organization-name: University of Washington url: http://depts.washington.edu/biowww/ [Instance] id: ORG:000074 type: developer name: University of Tennessee Genome Science and Technology url: http://gst.tennessee.edu [Instance] id: ORG:000075 type: developer name: Molecular Genetics and Bioinformatic Laboratory organization-name: University of Sao Paolo url: http://gdm.fmrp.usp.br country-name: Brazil [Instance] id: ORG:000076 type: developer name: Columbia University url: http://www.columbia.edu [Instance] id: ORG:000077 type: developer name: Bio-Medical Informatics Laboratory organization-name: Politecnico di Milano url: http://www.medinfopoli.polimi.it locality: Milan country-name: Italy [Instance] id: ORG:000078 type: developer name: National Library of Medicine url: http://www.nlm.nih.gov [Instance] id: ORG:000079 type: developer name: Livestock Issues Research Unit organization-name: USDA Agricultural Research Service url: http://liru.ars.usda.gov [Instance] id: ORG:000080 type: developer name: The Institute for Genomic Research url: http://www.tigr.org [Instance] id: ORG:000081 type: developer name: Lewis-Sigler Institute for Integrative Genomics organization-name: Princeton University url: http://genomics.princeton.edu [Instance] id: ORG:000082 type: developer name: University of Tennessee Health Science Center url: http://www.utmem.edu [Instance] id: ORG:000083 type: developer name: Georgetown University Medical Center Liu Lab url: http://gauss.dbb.georgetown.edu/liblab [Instance] id: ORG:000084 type: developer name: Bork group organization-name: European Molecular Biology Laboratory url: http://www.bork.embl-heidelberg.de [Instance] id: ORG:000085 type: developer name: Universidad Complutense de Madrid url: http://www.ucm.es country-name: Spain [Instance] id: ORG:000086 type: developer name: European Bioinformatics Institute url: http://www.ebi.ac.uk country-name: UK [Instance] id: ORG:000087 type: developer name: University of Amsterdam url: http://www.english.uva.nl country-name: Holland [Instance] id: ORG:000088 type: developer name: EcoliWiki url: http://ecoliwiki.org