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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/ https://doi.org/10.17616/R36R54 https://doi.org/10.17616/R36R54 |
SCR_008007 | 2026-02-14 02:06:41 | 1112 | |||||
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OncoboxPD Resource Report Resource Website 1+ mentions |
OncoboxPD (RRID:SCR_023723) | data or information resource, database | Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways. | Gene Ontology terms enrichment patterns, human molecular pathways, curated collection, GO terms enrichment patterns, experimental expression data analysis, |
is related to: oncoboxlib is related to: Gene Ontology |
Russian Science Foundation ; National Natural Science Foundation of China ; Qingdao Key Research Project ; Qingdao Key Health Discipline Development Fund |
PMID:35615022 | Free, Freely available | SCR_023723 | Oncobox Pathway Databank | 2026-02-14 02:06:35 | 3 | |||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | data or information resource, ontology, controlled vocabulary | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/ http://bioportal.bioontology.org/ontologies/ECO |
SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-02-14 02:05:01 | 19 | |||||
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PhenoGO Resource Report Resource Website 1+ mentions |
PhenoGO (RRID:SCR_013646) | data or information resource, database | PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA). |
uses: WormBase uses: SGD uses: Gene Ontology uses: Mouse Genome Informatics (MGI) uses: FlyBase is related to: WormBase is related to: SGD is related to: Gene Ontology is related to: Mouse Genome Informatics (MGI) is related to: FlyBase has parent organization: University of Arizona; Arizona; USA |
Available to the research community, Acknowledgement requested | nlx_152722 | www.phenogo.org | SCR_013646 | Phenotype Context Database for Gene Ontology Annotations | 2026-02-14 02:06:20 | 2 | ||||||||
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dcGO Resource Report Resource Website 10+ mentions |
dcGO (RRID:SCR_014392) | data or information resource, database | A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources. | database, mining, domain centric ontology, phenotype, human disease, drug, biomedical ontology, protein domain, hierarchy |
uses: Gene Ontology has parent organization: University of Bristol; Bristol; United Kingdom |
PMID:23161684 | Acknowledgement required, Both flat files and MySQL tables are available for download | SCR_014392 | 2026-02-14 02:06:21 | 27 | |||||||||
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Semantic Measures Library Resource Report Resource Website |
Semantic Measures Library (RRID:SCR_001383) | SML | software library, software toolkit, software resource | Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology). | semantic measure, semantic similarity, semantic relatedness, functional similarity, gene ontology, annotation, parse, gene, disease ontology, mesh, rdf, owl, umls, snomed-ct, java, semantic, command line |
is listed by: FORCE11 is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Ecole des Mines d'Ales; Ales; France |
Ecole des Mines d'Ales; Ales; France ; LGI2P Research Center |
PMID:24108186 | Free, Available for download, Freely available | nlx_152555 | http://www.semantic-measures-library.org | SCR_001383 | SML-Toolkit, Semantic Measures Library and ToolKit, Semantic Measures Library & ToolKit | 2026-02-15 09:18:05 | 0 | ||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | software application, source code, data analysis service, data processing software, software resource, database, service resource, production service resource, data or information resource, analysis service resource, data analysis software | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-02-15 09:18:10 | 2091 | |||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | nif-0000-20935, OMICS_02266 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-02-15 09:18:14 | 1242 | ||||
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High-Throughput GoMiner Resource Report Resource Website 1+ mentions |
High-Throughput GoMiner (RRID:SCR_000173) | web application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. | term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GoMiner has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
NCI 1Z01BC010842-01 | PMID:15998470 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149300 | SCR_000173 | 2026-02-15 09:17:53 | 2 | |||||||
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GONUTS Resource Report Resource Website 1+ mentions |
GONUTS (RRID:SCR_000653) | GONUTS | database, data or information resource, narrative resource, wiki | A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase... | ontology or annotation browser, ontology or annotation search engine, ontology or annotation editor, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: EcoliHub |
NIGMS 1U24 GM077905-01; NIGMS U24 GM088849 |
PMID:22110029 | Free for academic use, The community can contribute to this resource | OMICS_02268, nlx_30164 | SCR_000653 | Gene Ontology Normal Usage Tracking System, GONUTS wiki | 2026-02-15 09:17:58 | 1 | |||||
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Aging Portal Resource Report Resource Website |
Aging Portal (RRID:SCR_000496) | Aging | portal, database, catalog, data or information resource, topical portal | Portal devoted to aging relevant scientific data and resources. | late adult human, senescence |
uses: Aging Genes and Interventions Database uses: anage uses: Human Life-Table Database uses: Gene Ontology uses: Grants.gov uses: Integrated Blogs uses: Integrated Clinical Trials uses: Integrated Videos uses: Integrated Grants uses: Lifespan Observations Database uses: One Mind Biospecimen Bank Listing uses: Gait in Parkinson's Disease uses: SciCrunch Registry has parent organization: SciCrunch |
Aging | NIA 1R03AG043018-01 | Restricted | nlx_158366 | SCR_000496 | 2026-02-15 09:17:56 | 0 | ||||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | data analysis service, database, service resource, storage service resource, production service resource, data repository, data or information resource, analysis 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 | 2026-02-15 09:18:47 | 118 | |||||
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QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | database, ontology, software resource, data access protocol, web service, data or information resource, controlled vocabulary | 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 | 2026-02-15 09:18:51 | 523 | ||||
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Open PHACTS Resource Report Resource Website 10+ mentions |
Open PHACTS (RRID:SCR_005050) | OPS | organization portal, portal, database, software resource, consortium, data or information 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 | 2026-02-15 09:18:53 | 11 | ||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | web service, data access protocol, service resource, software resource | 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 | 2026-02-15 09:18:56 | 5 | ||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | source code, data analysis service, software resource, service resource, production service resource, analysis service resource | 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 | 2026-02-15 09:19:11 | 0 | |||||
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FunCluster Resource Report Resource Website 1+ mentions |
FunCluster (RRID:SCR_005774) | FunCluster | software application, data processing software, data analysis software, 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 | 2026-02-15 09:19:03 | 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 | source code, data analysis service, software resource, service resource, production service resource, analysis service resource | 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 | 2026-02-15 09:19:03 | 82 | |||||
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GOHyperGAll Resource Report Resource Website 1+ mentions |
GOHyperGAll (RRID:SCR_005766) | GOHyperGAll | software application, data processing software, data analysis software, software resource | 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. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, slimmer-type tool |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at Riverside; California; USA |
PMID:18354039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149267 | SCR_005766 | 2026-02-15 09:19:11 | 4 | |||||||
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FastSemSim Resource Report Resource Website 1+ mentions |
FastSemSim (RRID:SCR_006919) | FastSemSim | software library, software toolkit, software resource | A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, functional similarity, semantic similarity, graphical user interface, gene ontology, annotation, parse, gene, protein |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Padua; Padua; Italy has parent organization: SourceForge |
Open unspecified license - Free for academic use. GNU GPL license. However, This software is currently unpublished work. You must contact us before using it or its results or any work/app. based on top of it in any published work. | nlx_149309 | SCR_006919 | 2026-02-15 09:19:24 | 6 |
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