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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Gene Expression Profile Analysis Suite Resource Report Resource Website 10+ mentions |
Gene Expression Profile Analysis Suite (RRID:SCR_008341) | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. | expression, gene, analysis, genomic, microarray, microarray platform, prediction, data set |
is listed by: 3DVC has parent organization: Principe Felipe Research Centre; Valencia; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25201 | SCR_008341 | SciCrunch Registry | Gepas | 2026-10-24 12:49:54 | 20 | ||||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, data processing software, software application, software resource | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | SciCrunch Registry | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-10-24 12:46:15 | 8 | |||||
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Rice Gene Thresher Resource Report Resource Website 1+ mentions |
Rice Gene Thresher (RRID:SCR_007893) | data or information resource, database | A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | has parent organization: Kasetsart University; Bangkok; Thailand | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_007893 | SciCrunch Registry | Rice Gene Thresher | 2026-10-24 12:50:50 | 3 | ||||||||||
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Bio Resource for Array Genes Database Resource Report Resource Website |
Bio Resource for Array Genes Database (RRID:SCR_000748) | data or information resource, database | Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona. | drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissue | has parent organization: University of Arizona; Arizona; USA | nif-0000-10165 | SCR_000748 | SciCrunch Registry | BioRag | 2026-10-24 12:50:18 | 0 | |||||||||
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Dictyostelium Anatomy Ontology Resource Report Resource Website 1+ mentions |
Dictyostelium Anatomy Ontology (RRID:SCR_005929) | controlled vocabulary, data or information resource, ontology | An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT) | stricture, cell type, life cycle, phenotype, gene expression | has parent organization: Dictyostelium discoideum genome database | Wellcome Trust ; NIGMS GM64426; NHGRI HG00022 |
PMID:18366659 | nlx_14988 | SCR_005929 | SciCrunch Registry | 2026-10-24 12:45:35 | 1 | ||||||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | SciCrunch Registry | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-10-24 12:49:08 | 2 | |||||
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Ontology Lookup Service Resource Report Resource Website 10+ mentions |
Ontology Lookup Service (RRID:SCR_006596) | OLS | data access protocol, data or information resource, database, software resource, source code, web service | Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory. | ontology, ontology or annotation browser, ontology or annotation search engine, gold standard |
lists: Cell Type Ontology is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO-Edit is related to: OBO has parent organization: European Bioinformatics Institute |
BBSRC ; iSPIDER ; European Union FP6 Felics contract 021902 (RII3) |
PMID:18467421 PMID:16507094 |
Apache License, v2, Acknowledgement requested | OMICS_02275, nif-0000-10390, r3d100010413 | https://doi.org/10.17616/R3GS9G | http://www.ebi.ac.uk/ols | SCR_006596 | SciCrunch Registry | OLS - Ontology Lookup Service, Ontology Lookup Service (OLS) | 2026-10-24 12:45:45 | 24 | |||
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REViGO Resource Report Resource Website 1000+ mentions |
REViGO (RRID:SCR_005825) | REViGO | analysis service resource, data analysis service, production service resource, service resource | Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, visualization, statistical analysis, ontology or annotation visualization |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Rudjer Boskovic Institute; Zagreb; Croatia |
PMID:21789182 PMID:20585573 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02283, nlx_149332 | SCR_005825 | SciCrunch Registry | Reduce + Visualize Gene Ontology, REViGO - Reduce Visualize Gene Ontology, REViGO - Reduce & Visualize Gene Ontology, REViGO - Reduce and Visualize Gene Ontology, REViGO - Reduce + Visualize Gene Ontology | 2026-10-24 12:50:36 | 2430 | ||||||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | OMICS_02266, nif-0000-20935 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | SciCrunch Registry | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-10-24 12:44:40 | 1285 | ||||
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Generic GO Term Mapper Resource Report Resource Website 10+ mentions |
Generic GO Term Mapper (RRID:SCR_005806) | GOTermMapper, GO Term Mapper | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, gene association, slim ontology, slimmer-type tool, term enrichment, gene annotation, genomics, ontology, process, function, component, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA |
Free for academic use | nlx_149294, biotools:go_term_mapper | https://bio.tools/go_term_mapper | SCR_005806 | SciCrunch Registry | Generic Gene Ontology Term Mapper, Generic Gene Ontology (GO) Term Mapper | 2026-10-24 12:49:07 | 45 | ||||||
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GOA Resource Report Resource Website 500+ mentions |
GOA (RRID:SCR_007691) | GOA, GOA REF | data or information resource, database | An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website. | gene ontology, chicken proteome, cow proteome, human proteome, xref, gene, gene association, gold standard |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: FlyMine is related to: UniProt DAS is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures has parent organization: European Bioinformatics Institute |
Public, Available to the research community, All UniProtKB-GOA Gene Association Files are released approximately every four weeks | nif-0000-02916 | SCR_007691 | SciCrunch Registry | UniProtKB-GOA, Gene Ontology Annotation (UniProtKB-GOA) Database, GOA - Gene Ontology Annotation, Gene Ontology Annotation, GO Annotation at EBI | 2026-10-24 12:50:47 | 678 | |||||||
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Generic GO Term Finder Resource Report Resource Website 100+ mentions |
Generic GO Term Finder (RRID:SCR_008870) | GOTermFinder, GO-TermFinder, GO Term Finder, GO::TermFinder | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource, source code | The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, graph, visualization, genomics, gene association, ontology or annotation visualization, term enrichment, ontology, process, function, component, enrichment, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA has parent organization: Comprehensive Perl Archive Network |
NHGRI 1R01HG002732 | PMID:15297299 | Free for academic use | nlx_149293, biotools_go_term_finder | https://bio.tools/go_term_finder | SCR_008870 | SciCrunch Registry | Generic Gene Ontology (GO) Term Finder, Generic Gene Ontology Term Finder | 2026-10-24 12:46:11 | 108 | ||||
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GOCat Resource Report Resource Website 1+ mentions |
GOCat (RRID:SCR_003608) | GOCat | analysis service resource, data analysis service, production service resource, service resource, software resource | Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances. | machine learning, classification |
is related to: Gene Ontology has parent organization: University of Geneva; Geneva; Switzerland |
PMID:23842461 | nlx_157764 | SCR_003608 | SciCrunch Registry | GOCat the Gene Ontology Categorizer, GOCat - the Gene Ontology Categorizer | 2026-10-24 12:44:59 | 2 | |||||||
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DynGO Resource Report Resource Website 1+ mentions |
DynGO (RRID:SCR_007009) | DynGO | software resource | DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible | gene, annotation, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
NSF IIS-0430743 | PMID:16091147 | Free for academic use | nlx_149118 | http://gauss.dbb.georgetown.edu/liblab | SCR_007009 | SciCrunch Registry | DynGO: a tool for visualizing and mining of Gene Ontology and its associations | 2026-10-24 12:45:52 | 6 | ||||
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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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GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | SciCrunch Registry | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-10-24 12:45:30 | 0 | ||||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | SciCrunch Registry | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-10-24 12:49:08 | 353 | ||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | data processing software, software application, software resource | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | SciCrunch Registry | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-10-24 12:49:52 | 122 | |||||
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CLENCH Resource Report Resource Website 1+ mentions |
CLENCH (RRID:SCR_005735) | CLENCH | data processing software, software application, software resource, source code | Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible, | gene, microarray, function, functional categorization, statistical analysis, slimmer-type tool, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: TAIR has parent organization: Stanford Center for Biomedical Informatics Research |
PMID:14764555 | Free for academic use | nlx_149216 | http://www.personal.psu.edu/nhs109/Clench | SCR_005735 | SciCrunch Registry | CLENCH - Cluster Enrichment, CLENCH: A program for calculating cluster enrichment using the Gene Ontology, Cluster Enrichment, Cluster Enrichment (CLENCH) | 2026-10-24 12:45:31 | 4 | |||||
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MetaGeneProfiler Resource Report Resource Website |
MetaGeneProfiler (RRID:SCR_005794) | MetaGP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online tool | gene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Institute of Statistical Mathematics; Tokyo; Japan |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149271 | SCR_005794 | SciCrunch Registry | Meta Gene Profiler, MetaGeneProfiler on the WEB, Meta Gene Profiler (MetaGP), MetaGeneProfiler on the WEB - Web service for significance test of differentially-expressed Meta Genes | 2026-10-24 12:50:36 | 0 |
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
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