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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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gsGator Resource Report Resource Website |
gsGator (RRID:SCR_012035) | gsGator | analysis service resource, data analysis service, production service resource, service resource | A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks. | linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, function |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:24423189 | Free, Public | OMICS_02233 | SCR_012035 | SciCrunch Registry | 2026-10-24 12:51:04 | 0 | |||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, data or information resource, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | SciCrunch Registry | 2026-10-24 12:51:05 | 1 | |||||
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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 | SciCrunch Registry | Phenotype Context Database for Gene Ontology Annotations | 2026-10-24 12:51:08 | 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 | SciCrunch Registry | 2026-10-24 12:51:09 | 27 | |||||||||
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FSST - Functional Similarity Search Tool Resource Report Resource Website |
FSST - Functional Similarity Search Tool (RRID:SCR_005819) | FSST | software application, software resource | The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | other analysis, functional similarity search, annotation, ontology, java, training tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GOTaxExplorer has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
BMBF 016R0453; DFG KFO 129/1-1; European Union F6 contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149320 | SCR_005819 | SciCrunch Registry | Functional Similarity Search Tool (FSST), Functional Similarity Search Tool | 2026-10-24 12:51:26 | 0 | |||||
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Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software repository, software resource, software toolkit | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | SciCrunch Registry | 2026-10-24 12:51:28 | 24163 | |||||||
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FuncExpression Resource Report Resource Website |
FuncExpression (RRID:SCR_005773) | FuncExpression | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 11, 2012. 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. Platform: Online tool | statistical analysis, genomics, compare, function, plant, animal, fungus, gene, proteomics, gene expression, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: PLEXdb - Plant Expression Database has parent organization: Iowa State University; Iowa; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149237 | SCR_005773 | SciCrunch Registry | 2026-10-24 12:50:36 | 0 | ||||||||
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ProfCom - Profiling of complex functionality Resource Report Resource Website 1+ mentions |
ProfCom - Profiling of complex functionality (RRID:SCR_005797) | ProfCom | analysis service resource, data analysis service, production service resource, service resource | Profiling of Complex Functionality (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. Platform: Online tool | gene, function, profile, gene ontology, complex function, 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: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
DFG | PMID:16959266 | Free for academic use | biotools:profcom, nlx_149276 | https://bio.tools/profcom | SCR_005797 | SciCrunch Registry | Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) | 2026-10-24 12:50:36 | 4 | ||||
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SerbGO Resource Report Resource Website |
SerbGO (RRID:SCR_005798) | SerbGO | analysis service resource, data analysis service, production service resource, service resource | 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. Platform: Online tool | microarray, gene expression, statistical analysis, gene ontology, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Barcelona; Barcelona; Spain |
PMID:18480123 | Free for academic use | nlx_149286, biotools:serbgo | https://bio.tools/serbgo | SCR_005798 | SciCrunch Registry | SerbGO - Searching the best GO Tool | 2026-10-24 12:50:36 | 0 | |||||
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GOtcha Resource Report Resource Website 1+ mentions |
GOtcha (RRID:SCR_005790) | GOtcha | analysis service resource, data analysis service, production service resource, service resource | GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool | function, protein, prediction, genome, annotation, gene, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Dundee; Scotland; United Kingdom |
Wellcome Trust 060269; European Union fifth framework QLRI-CT-2000-00127 |
PMID:15550167 | Free for academic use | nlx_149269 | http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html | SCR_005790 | SciCrunch Registry | 2026-10-24 12:50:36 | 3 | |||||
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GoAnnotator Resource Report Resource Website 1+ mentions |
GoAnnotator (RRID:SCR_005792) | GOAnnotator | analysis service resource, data analysis service, production service resource, service resource | A tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tool | text mining, protein, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt has parent organization: University of Lisbon; Lisbon; Portugal |
European Union contract QLRI-1999-50595 | PMID:17181854 | Free for academic use | nlx_149303 | SCR_005792 | SciCrunch Registry | 2026-10-24 12:50:36 | 1 | ||||||
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GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, database, service resource | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. 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. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | SciCrunch Registry | 2026-10-24 12:50:36 | 29 | |||||
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GOSlimViewer Resource Report Resource Website 10+ mentions |
GOSlimViewer (RRID:SCR_005665) | GOSlimViewer | analysis service resource, data analysis service, production service resource, service resource | Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. | agriculture, browser, slimmer-type tool, gene ontology, gene, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149103, OMICS_02270 | SCR_005665 | SciCrunch Registry | GO Slim Viewer, GOSlim Viewer | 2026-10-24 12:50:35 | 40 | |||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. 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. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | SciCrunch Registry | Expression Profiler at the EBI | 2026-10-24 12:50:36 | 6 | ||||
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GOChase Resource Report Resource Website 1+ mentions |
GOChase (RRID:SCR_005822) | GOChase | analysis service resource, data analysis service, production service resource, service resource | GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool | other analysis, historical views of go, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Seoul National University College of Medicine; Seoul; South Korea |
Ministry of Health and Welfare - Republic of Korea 0405-BC0206040004 | PMID:15513987 | Free for academic use | nlx_149324 | SCR_005822 | SciCrunch Registry | GOChase: correcting errors from gene ontology-based annotations for gene products | 2026-10-24 12:50:36 | 1 | |||||
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SGD Gene Ontology Slim Mapper Resource Report Resource Website 10+ mentions |
SGD Gene Ontology Slim Mapper (RRID:SCR_005784) | GO Slim Mapper | analysis service resource, data analysis service, production service resource, service resource | 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. Three GO Slim sets are available at SGD: * Macromolecular complex terms: protein complex terms from the Cellular Component ontology * Yeast GO-Slim: GO terms that represent the major Biological Processes, Molecular Functions, and Cellular Components in S. cerevisiae * Generic GO-Slim: broad, high level GO terms from the Biological Process and Cellular Component ontologies selected and maintained by the Gene Ontology Consortium (GOC) Platform: Online tool | gene, annotation, gene ontology, protein complex, biological process, molecular function, cellular component, gene ontology, orf, yeast, statistical analysis, slimmer-type tool, function |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: SGD |
Free for academic use | nlx_149258 | SCR_005784 | SciCrunch Registry | GO Term Mapper, Gene Ontology Slim Mapper | 2026-10-24 12:50:36 | 31 | |||||||
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GO-Module Resource Report Resource Website 1+ mentions |
GO-Module (RRID:SCR_005813) | GO-Module | analysis service resource, data analysis service, production service resource, service resource | GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool | functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: AmiGO has parent organization: University of Illinois at Chicago; Illinois; USA |
NIH ; Cancer Research Foundation ; NLM K22 LM008308; NCI 1U54CA121852; NCRR UL1 RR024999 |
PMID:21421553 | Free for academic use | nlx_149322 | SCR_005813 | SciCrunch Registry | Hierarchical optimization of enriched GO terms | 2026-10-24 12:50:36 | 3 | |||||
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GOanna Resource Report Resource Website 10+ mentions |
GOanna (RRID:SCR_005684) | GOanna | analysis service resource, data analysis service, production service resource, service resource | 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 of GO annotated proteins. 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. Platform: Online tool | agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149139 | SCR_005684 | SciCrunch Registry | AgBase GOanna | 2026-10-24 12:50:35 | 17 | |||||
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FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products Resource Report Resource Website |
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products (RRID:SCR_005738) | FuSSiMeG | analysis service resource, data analysis service, production service resource, service resource | FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool | protein, similarity, gene ontology, gene, ontology, statistical analysis, term enrichment, semantic similarity, analysis, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: ProteInOn has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149198 | SCR_005738 | SciCrunch Registry | Functional Semantic Similarity Measure between Gene-Products, Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) | 2026-10-24 12:50:35 | 0 | |||||||
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Mouse Genome Informatics (MGI) Resource Report Resource Website 1000+ mentions |
Mouse Genome Informatics (MGI) (RRID:SCR_006460) | MGI | data or information resource, database | International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. | RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Cytokine Registry is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is listed by: NIH Data Sharing Repositories is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: MONARCH Initiative is related to: MouseCyc is related to: AmiGO is related to: Gene Expression Database is related to: Bgee: dataBase for Gene Expression Evolution is related to: HomoloGene is related to: Rat Gene Symbol Tracker is related to: Enhancer Trap Line Browser is related to: Integrated Brain Gene Expression is related to: MalaCards is related to: Gene Ontology is related to: BioMart Project is related to: NIH Data Sharing Repositories is related to: RIKEN integrated database of mammals is related to: JAX Neuroscience Mutagenesis Facility is related to: PhenoGO is related to: International Mouse Strain Resource is related to: Mouse Genome Database is related to: Mouse Tumor Biology Database has parent organization: Jackson Laboratory is parent organization of: Anatomy of the Laboratory Mouse is parent organization of: Mouse Genome Informatics Transgenes is parent organization of: Federation of International Mouse Resources is parent organization of: MGI GO Browser is parent organization of: Recombinase (cre) Activity is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource is parent organization of: MGI strains is parent organization of: MPO is parent organization of: Phenotypes and Mutant Alleles is parent organization of: Human Mouse Disease Connection is parent organization of: Functional Annotation is parent organization of: Strains, SNPs and Polymorphisms is parent organization of: Vertebrate Homology is parent organization of: Batch Data and Analysis Tool is parent organization of: Nomenclature |
NCI CA089713; NHGRI HG000330; NHGRI HG002273; NHGRI P41 HD062499; NICHD HD033745 |
PMID:19274630 PMID:18428715 |
Free, Freely available | nif-0000-00096, OMICS_01656, r3d100010266 | http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml, http://www.informatics.jax.org/expression.shtml, https://doi.org/10.17616/R35P54 | SCR_006460 | SciCrunch Registry | , MGI, Mouse Genome Informatics | 2026-10-24 12:50:39 | 1220 |
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