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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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GOEAST - Gene Ontology Enrichment Analysis Software Toolkit Resource Report Resource Website 10+ mentions |
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) | GOEAST | analysis service resource, data analysis service, production service resource, service resource | Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool | statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, visualization, 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: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China 30725014; National Natural Science Foundation of China 90612019; Ministry of Science and Technology of China 2007CB946901; Chinese Academy of Sciences KSCX2-YW-R-134; Chinese Academy of Sciences KSCX2-YW-N-024 |
PMID:18487275 | Free for academic use | biotools:goeast, nlx_149248 | https://bio.tools/goeast | SCR_006580 | SciCrunch Registry | Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) | 2026-10-24 12:50:39 | 40 | ||||
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GeneTerm Linker Resource Report Resource Website 1+ mentions |
GeneTerm Linker (RRID:SCR_006385) | GTLinker | analysis service resource, data analysis service, production service resource, service resource | Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. | gene, functional annotation, function, functional metagroup, p-value, annotation, web service |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: InterPro has parent organization: Spanish National Research Council; Madrid; Spain |
PMID:21949701 | Acknowledgement requested | OMICS_02227 | SCR_006385 | SciCrunch Registry | GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage | 2026-10-24 12:50:39 | 2 | ||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | analysis service resource, data analysis service, production service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | SciCrunch Registry | 2026-10-24 12:50:38 | 114 | ||||||
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Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. | gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: ArrayExpress is related to: Plant Ontology is related to: Gene Ontology has parent organization: Ghent University; Ghent; Belgium |
PMID:24407224 | biotools:magic, OMICS_02206 | https://bio.tools/magic | SCR_006406 | SciCrunch Registry | MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium | 2026-10-24 12:50:39 | 709 | ||||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | SciCrunch Registry | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-10-24 12:50:40 | 524 | |||||
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AnimalTFDB Resource Report Resource Website 100+ mentions |
AnimalTFDB (RRID:SCR_001624) | AnimalTFDB | data or information resource, database | A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Ensembl has parent organization: Huazhong University of Science and Technology; Wuhan; China |
Huazhong University of Science and Technology; Wuhan; China ; Fundamental Research Funds for the Central Universities 2010MS045; National Natural Science Foundation of China 31171271 |
PMID:22080564 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01856, nlx_153892, biotools:animal_tfdb | https://bio.tools/animal_tfdb | SCR_001624 | SciCrunch Registry | Animal Transcription Factor Database | 2026-10-24 12:50:20 | 292 | ||||
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Automated Microarray Pipeline Resource Report Resource Website |
Automated Microarray Pipeline (RRID:SCR_001219) | AMP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. | microarray, normalization |
is listed by: OMICtools is related to: Gene Ontology has parent organization: TM4 |
NLM R01-LM008795 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02125 | http://www.tm4.org/amp.html | SCR_001219 | SciCrunch Registry | TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP | 2026-10-24 12:50:19 | 0 | |||||
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WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. | subcellular localization, protein |
is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01636 | SCR_001402 | SciCrunch Registry | weighted gene ontology term based subcellular locallization prediction | 2026-10-24 12:50:20 | 4 | |||||||
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CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | data or information resource, data set, service resource | With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool | gene, biological process, cellular component, molecular function, browser, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Cancer Genome Anatomy Project |
NCI | Free for academic use | nlx_149116 | SCR_005676 | SciCrunch Registry | Cancer Genome Anatomy Project GO Browser | 2026-10-24 12:45:30 | 4 | ||||||
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Onto-Express Resource Report Resource Website 50+ mentions |
Onto-Express (RRID:SCR_005670) | OE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, biochemical function, biological process, cellular role, cellular component, molecular function, chromosome location, java, data-mining, browser, visualization, analysis, statistical analysis, term enrichment, search engine, other analysis, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, custom level of abstraction of the gene ontology, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
Wayne State University School of Medicine; Michigan; USA ; NICHD HD36512 |
PMID:12620386 PMID:11829497 PMID:15215428 |
Free for academic use | nlx_149110 | http://vortex.cs.wayne.edu:8080 | SCR_005670 | SciCrunch Registry | Onto-Express (OE) | 2026-10-24 12:45:30 | 85 | ||||
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GeneTools Resource Report Resource Website 1000+ mentions |
GeneTools (RRID:SCR_005663) | GeneTools | data access protocol, data or information resource, software resource, web service | Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology. | genome-wide analyses, annotation, gene, visualization, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, statistical analysis, term enrichment, browser, search engine, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Norwegian University of Science and Technology; Trondheim; Norway is parent organization of: GeneTools: explore GeneOntology |
National Council on Cardiovascular Diseases ; Norwegian Research Council ; Norwegian University of Science and Technology |
PMID:17062145 | SCR_002911, SCR_007388, nif-0000-00407, nif-0000-30011, nlx_149102 | SCR_005663 | SciCrunch Registry | 2026-10-24 12:45:30 | 1753 | |||||||
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go-perl Resource Report Resource Website 10+ mentions |
go-perl (RRID:SCR_005730) | go-perl | software resource | go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, annotation, software library, slimmer-type tool, parser |
is listed by: Gene Ontology Tools is related to: OBO is related to: go-moose is related to: go-db-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149190 | SCR_005730 | SciCrunch Registry | 2026-10-24 12:45:32 | 11 | ||||||||
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go-db-perl Resource Report Resource Website 1+ mentions |
go-db-perl (RRID:SCR_005721) | go-db-perl | software resource | Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, database, gene ontology, database or data warehouse |
is listed by: Gene Ontology Tools is related to: AmiGO is related to: go-moose is related to: Ensembl is related to: go-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149180 | SCR_005721 | SciCrunch Registry | 2026-10-24 12:45:31 | 1 | ||||||||
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Manatee Resource Report Resource Website 50+ mentions |
Manatee (RRID:SCR_005685) | Manatee | software resource | Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris | gene, genome, annotation, ontology or annotation browser, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: SourceForge |
Open unspecified license - Free for academic use | nlx_149128 | SCR_005685 | SciCrunch Registry | 2026-10-24 12:45:30 | 64 | ||||||||
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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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GOdist Resource Report Resource Website |
GOdist (RRID:SCR_005770) | GOdist | data analysis software, data processing software, software application, software resource | GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, function, gene, gene expression, gene ontology, matlab, affymetrix, microarray, biological process, molecular function, cellular component, fisher exact test, kolmogorov-smirnov |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:15550480 | Free for academic use | nlx_149260 | SCR_005770 | SciCrunch Registry | 2026-10-24 12:45:32 | 0 | |||||||
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Ontologizer Resource Report Resource Website 100+ mentions |
Ontologizer (RRID:SCR_005801) | Ontologizer | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource, source code | The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, biological data, gene ontology, statistical analysis, fisher exact test, visualization, graph, java, annotation, parent-child, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
DFG SFB 760 | PMID:18511468 PMID:17848398 |
Free for academic use | nlx_149289 | SCR_005801 | SciCrunch Registry | The Ontologizer | 2026-10-24 12:45:33 | 124 | |||||
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THEA - Tools for High-throughput Experiments Analysis Resource Report Resource Website |
THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) | THEA | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, analysis, ontology, microarray, genomic, annotation, gene ontology, data mining, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Virtual Biology Lab |
French Ministry of Higher Education and Research ; Bioinformatic Program |
PMID:15130932 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149290 | SCR_005802 | SciCrunch Registry | Tools for High-throughput Experiments Analysis | 2026-10-24 12:45:32 | 0 | |||||
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PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | data or information resource, database, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotate, editor, literature curation tool, literature, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR has parent organization: Stanford University; Stanford; California |
NHGRI R01HG02728 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149338 | SCR_005830 | SciCrunch Registry | 2026-10-24 12:45:33 | 1 | |||||||
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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | data analysis software, data processing software, software application, software resource | MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible | gene, gene ontology, gene association, gene expression, profile, microarray, pathway, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at San Francisco; California; USA has parent organization: Gene Map Annotator and Pathway Profiler |
University of California at San Francisco; California; USA ; San Francisco General Hospital; California; USA ; NHLBI ; NCRR MO1RR00083 |
PMID:12540299 | Free for academic use | nlx_149270 | SCR_005791 | SciCrunch Registry | 2026-10-24 12:45:32 | 26 |
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