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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | controlled vocabulary, ontology, data or information resource | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-07-27 09:32:00 | 44 | |||||
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Repository of molecular brain neoplasia data Resource Report Resource Website 1+ mentions |
Repository of molecular brain neoplasia data (RRID:SCR_004704) | REMBRANDT | service resource, data analysis service, database, analysis service resource, topical portal, production service resource, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype |
is related to: Gene Ontology is related to: Glioma Molecular Dignostic Initiatives has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI ; NINDS |
PMID:19208739 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00230 | SCR_004704 | REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) | 2026-07-27 09:32:06 | 2 | ||||
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PANTHER Resource Report Resource Website 5000+ mentions |
PANTHER (RRID:SCR_004869) | PANTHER | ontology, service resource, data analysis service, database, controlled vocabulary, analysis service resource, production service resource, data or information resource | System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | hidden markov model, human, mouse, genome, protein, gene, function, pathway, ortholog, phylogenetic tree, gene ortholog, protein family, gene function, evolution, data set, molecular function, biological process, cellular component, transcript, FASEB list |
is used by: NIF Data Federation is used by: YPED is used by: EMBRYS is related to: Gene Ontology is related to: Pathway Commons is related to: KOBAS has parent organization: University of Southern California; Los Angeles; USA is parent organization of: PANTHER Evolutionary analysis of coding SNPs |
NIGMS GM081084 | PMID:23193289 PMID:20015972 PMID:12952881 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015893, nlx_84521 | SCR_004869 | PANTHER Classification System, Protein ANalysis THrough Evolutionary Relationships Classification System, Protein ANalysis THrough Evolutionary Relationships, PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System | 2026-07-27 09:32:08 | 8331 | |||||
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GOdist Resource Report Resource Website |
GOdist (RRID:SCR_005770) | GOdist | software application, software resource, data processing software, data analysis software | 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 | 2026-07-27 09:32:22 | 0 | |||||||
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Ontologizer Resource Report Resource Website 100+ mentions |
Ontologizer (RRID:SCR_005801) | Ontologizer | service resource, data analysis service, analysis service resource, software resource, source code, software application, production service resource, data processing software | 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 | The Ontologizer | 2026-07-27 09:32:22 | 122 | |||||
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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 | software application, software resource, data processing software, data analysis software | 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 | Tools for High-throughput Experiments Analysis | 2026-07-27 09:32:22 | 0 | |||||
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CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | service resource, data or information resource, data set | 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 | Cancer Genome Anatomy Project GO Browser | 2026-07-27 09:32:20 | 4 | ||||||
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PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | service resource, database, data or information 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 | 2026-07-27 09:32:23 | 1 | |||||||
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Onto-Express Resource Report Resource Website 50+ mentions |
Onto-Express (RRID:SCR_005670) | OE | service resource, data analysis service, database, analysis service resource, production service resource, data or information 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 | Onto-Express (OE) | 2026-07-27 09:32:20 | 85 | ||||
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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | software application, software resource, data processing software, data analysis software | 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 | 2026-07-27 09:32:22 | 26 | ||||||
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GeneTools Resource Report Resource Website 1000+ mentions |
GeneTools (RRID:SCR_005663) | GeneTools | web service, data access protocol, software resource, data or information resource | 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 University of Science and Technology ; Norwegian Research Council |
PMID:17062145 | SCR_002911, SCR_007388, nif-0000-00407, nif-0000-30011, nlx_149102 | SCR_005663 | 2026-07-27 09:32:20 | 1752 | |||||||
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GOArray Resource Report Resource Website 1+ mentions |
GOArray (RRID:SCR_005785) | GOArray | software application, software resource, data processing software, data analysis software | GOArray is a Perl program which inputs a lists of genes annotated as of interest (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, gene, visualization, gene ontology, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Yale School of Medicine; Connecticut; USA |
Free for academic use | nlx_149259 | http://goarray.med.yale.edu/GOArray/ | SCR_005785 | 2026-07-27 09:32:22 | 1 | |||||||
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GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | service resource, data analysis service, database, analysis service resource, production service resource, data or information 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 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-07-27 09:32:20 | 0 | ||||||
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TrED Resource Report Resource Website 1+ mentions |
TrED (RRID:SCR_005869) | TrED | database, data analysis software, software resource, software application, data processing software, data or information resource | TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. | expressed sequence tag, transcriptional profile, fungal pathogen, bmu01672, chuv862.00, mya-3108, cdna, pathway, microarray, classification, blast, unisequence, peptide, annotation |
is related to: Gene Ontology is related to: KEGG is related to: GenBank is related to: Pfam |
Ministry of Science and Technology of China 2006AA020504 | PMID:17650345 | nlx_149408 | SCR_005869 | TrED - T. rubrum Expression Database, Trichophyton rubrum Expression Database, Trichophyton rubrum Expression Database (TrED) | 2026-07-27 09:32:24 | 5 | ||||||
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ConceptWiki Resource Report Resource Website 1+ mentions |
ConceptWiki (RRID:SCR_006362) | ConceptWiki | narrative resource, wiki, people resource, data or information resource | A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki. | wiki, community, concept, unambiguous, repository |
is used by: Open PHACTS is related to: Gene Ontology is related to: Unified Medical Language System is related to: UniProtKB |
Public, The community can contribute to this resource | nlx_152103 | http://www.conceptwiki.org/index.php/Main%20Page | SCR_006362 | 2026-07-27 09:32:32 | 3 | |||||||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | service resource, data analysis service, analysis service resource, software resource, production service resource | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-07-27 09:32:30 | 35 | |||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | service resource, database, d spatial image, storage service resource, image collection, data repository, data or information resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-07-27 09:32:55 | 7 | |||||
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Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | d visualization software, data visualization software, software resource, software application, data processing software | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-07-27 09:33:04 | 52 | ||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | software application, software resource, data processing software, data analysis software | 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 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-07-27 09:33:13 | 8 | |||||
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Gene Ontology Extension Resource Report Resource Website |
Gene Ontology Extension (RRID:SCR_010327) | GO-EXT | controlled vocabulary, ontology, data or information resource | An extension of the Gene Ontology. | obo |
is listed by: BioPortal has parent organization: Gene Ontology |
nlx_157414 | SCR_010327 | 2026-07-27 09:33:40 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
