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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-09-12 12:56:15 | 118 | |||||
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QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | controlled vocabulary, data access protocol, data or information resource, database, ontology, software resource, web service | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | Quick GO | 2026-09-12 12:56:14 | 556 | ||||
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Open PHACTS Resource Report Resource Website 10+ mentions |
Open PHACTS (RRID:SCR_005050) | OPS | consortium, data or information resource, database, organization portal, portal, software resource | Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data. | drug, enzyme family, structure, receptor, target, ki, pathway, pharmacology, enzyme, small molecule, data mining, annotation, drug discovery, drug development, pharmacological profile, pharmacokinetic, admet data, biological target, chemical, linked data, rdf, nanopublication, platform, semantic technology, text mining, bioinformatics, cheminformatics, interoperability, chemistry, data provenance, compound, small molecule, semantic integration, drug discovery |
uses: CHEBI uses: ChemSpider uses: ConceptWiki uses: DrugBank uses: ENZYME uses: UniProt uses: Gene Ontology uses: WikiPathways is listed by: Consortia-pedia is listed by: FORCE11 is related to: Nanopub.org is related to: eTRIKS is related to: Janssen Research and Development is related to: Almirall is related to: ESTEVE is related to: Merck is related to: Pfizer Animal Genetics is related to: VU University; Amsterdam; Netherlands is related to: European Bioinformatics Institute is related to: Maastricht University; Maastricht; Netherlands is related to: University of Bonn; Bonn; Germany is related to: Royal Society of Chemistry is related to: Spanish National Cancer Research Center is related to: Netherlands Bioinformatics Centre is related to: SIB Swiss Institute of Bioinformatics is related to: Technical University of Denmark; Lyngby; Denmark is related to: University of Santiago de Compostela; Santiago de Compostela; Spain is related to: University of Vienna; Vienna; Austria is related to: University of Hamburg; Hamburg; Germany is related to: University of Manchester; Manchester; United Kingdom is related to: BioSolveIT is related to: ConnectedDiscovery is related to: OpenLink Software is related to: SciBite is related to: Open PHACTS Foundation has parent organization: University of Vienna; Vienna; Austria |
Innovative Medicines Initiative grant 115191; EFPIA ; Open PHACTS Foundation |
PMID:22683805 | Open unspecified license, Registration required, Non-commercial | r3d100011550, nlx_144033 | https://www.force11.org/node/4684, http://www.imi.europa.eu/content/open-phacts, https://doi.org/10.17616/R3T63F | SCR_005050 | Open PHACTS - Open Pharmacological Space, OpenPhacts.org, Open Pharmacological Space, Open Pharmacological Concepts Triple Store, OpenPHACTS, Open PHACTS: Open Pharmacological Space | 2026-09-12 12:56:20 | 11 | ||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | data access protocol, service resource, software resource, web service | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-09-12 12:56:24 | 5 | ||||
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COBrA Resource Report Resource Website 1000+ mentions |
COBrA (RRID:SCR_005677) | COBrA | software resource | 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. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, anatomy, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC 15/BEP 17046 | PMID:15513995 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149117 | SCR_005677 | COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor | 2026-09-12 12:56:29 | 1396 | |||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-09-12 12:56:30 | 4535 | |||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | data analysis software, data processing software, software application, software resource | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-09-12 12:56:29 | 0 | ||||||||
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DBD - Slim Gene Ontology Resource Report Resource Website |
DBD - Slim Gene Ontology (RRID:SCR_005728) | Slim Gene Ontology | data or information resource, database, software application, software resource | Db for Dummies! is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree. The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from www.geneontology.org/GO.slims.shtml. Platform: Windows compatible | gene ontology, gene, hierarchy, visualization, database or data warehouse |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Db for Dummies! |
Free for academic use | nlx_149185 | SCR_005728 | Db for Dummies! - Slim Gene Ontology, Db for Dummies - Slim Gene Ontology | 2026-09-12 12:56:30 | 0 | |||||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-09-12 12:56:30 | 3 | |||||||
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ToppGene Suite Resource Report Resource Website 1000+ mentions |
ToppGene Suite (RRID:SCR_005726) | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, resource, service resource | ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. | gene portal, enrichment analysis, functional annotation, gene prioritization, protein interaction, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: NIDDK Information Network (dkNET) is listed by: GUDMAP Ontology is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: ToppCluster |
State of Ohio Computational Medicine Center ODD TECH 04-042; NIDDK 1U01DK70219; NIDDK P30DK078392 |
PMID:19465376 | Free for academic use | nlx_149183, biotools:toppgene_suite | https://bio.tools/toppgene_suite | SCR_005726 | ToppGene | 2026-09-12 12:56:30 | 1131 | |||||
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TAIR Keyword Browser Resource Report Resource Website 10+ mentions |
TAIR Keyword Browser (RRID:SCR_005687) | TAIR Keyword Browser | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | 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. Platform: Online tool | gene ontology, gene, publication, microarray, annotation, cellular component, biological process, molecular function, plant, growth, development, stage, anatomical entity, anatomy, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR |
Free for academic use | nlx_149132 | http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword | SCR_005687 | TAIR Keyword Search and Browse, The Arabidopsis Information Resource Keyword Browser | 2026-09-12 12:56:29 | 37 | ||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-09-12 12:56:30 | 0 | ||||||
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Onto-Miner Resource Report Resource Website |
Onto-Miner (RRID:SCR_005722) | OM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool | gene, annotation, search engine, database, analysis, ontology or annotation search engine, database or data warehouse, other analysis, scripted search of the onto-tools database for gene annotations |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 PMID:17584796 |
Free for academic use | nlx_149181 | SCR_005722 | Onto-Miner (OM) | 2026-09-12 12:56:30 | 0 | ||||||
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GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a 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. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-09-12 12:56:29 | 2 | |||||||
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Pandora - Protein ANnotation Diagram ORiented Analysis Resource Report Resource Website 1+ mentions |
Pandora - Protein ANnotation Diagram ORiented Analysis (RRID:SCR_005686) | Pandora | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | 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. Platform: Online tool | protein, annotation, mass spectrometry, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Israeli Ministry of Defense ; Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:14500825 | Free for academic use | nlx_149131 | SCR_005686 | Protein ANnotation Diagram ORiented Analysis | 2026-09-12 12:56:29 | 2 | |||||
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GOfetcher Resource Report Resource Website |
GOfetcher (RRID:SCR_005681) | GOfetcher | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool | gene, nucleotide, protein, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Southern Mississippi; Mississippi; USA |
NSF EPS-0556308; U.S. Army ; Environmental Quality Program contract #W912HZ-05-P-0145 |
PMID:18728045 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149124 | http://mcbc.usm.edu/gofetcher/ | SCR_005681 | GOfetcher: a database with complex searching facility for gene ontology | 2026-09-12 12:56:29 | 0 | ||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-12 12:56:29 | 1 | |||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. 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 (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-09-12 12:56:31 | 0 | |||||
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FunCluster Resource Report Resource Website 1+ mentions |
FunCluster (RRID:SCR_005774) | FunCluster | data analysis software, data processing software, software application, software resource | FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed 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. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genomic, gene, functional analysis, gene expression, cdna microarray, cdna, microarray, function, cluster, annotation, biological process, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Cordelier Research Center |
PMID:17007070 PMID:16506959 PMID:16046292 |
Free for academic use, GNU General Public License, v2 | nlx_149242, biotools:funcluster | https://bio.tools/funcluster | SCR_005774 | FunCluster R Package, FunCluster Algorithm | 2026-09-12 12:56:31 | 2 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-09-12 12:56:31 | 89 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
