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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | data or information resource, database | The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. | protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute |
NHGRI R01 HG004881; NIAID contract HHSN266200100038C |
PMID:22140108 | biotools:charprotdb, nlx_149421 | https://bio.tools/charprotdb | SCR_005872 | Characterized Protein Database | 2026-02-14 02:06:25 | 0 | |||||
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VirHostNet: Virus-Host Network Resource Report Resource Website 1+ mentions |
VirHostNet: Virus-Host Network (RRID:SCR_005978) | VirHostNet | data or information resource, database | Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy. | interaction, protein, virus, protein-protein interaction, protein interaction, infectious disease, antiviral drug design, proteome, interactome, molecular function, cellular pathway, protein domain, virus-virus, virus-host, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: VirusMINT is related to: IntAct is related to: HIV-1 Human Protein Interaction Database is related to: PSICQUIC Registry has parent organization: Claude Bernard University Lyon 1; Lyon; France |
PMID:18984613 | Acknowledgement requested, Public | nif-0000-03634, OMICS_01910, biotools:virhostnet | https://bio.tools/virhostnet | SCR_005978 | Virus-Host Network | 2026-02-14 02:05:53 | 6 | |||||
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HPRD - Human Protein Reference Database Resource Report Resource Website 1000+ mentions |
HPRD - Human Protein Reference Database (RRID:SCR_007027) | HPRD | data or information resource, database | Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. | protein, disease, network, post-translational, proteome, protein binding, protein s, protein c, pathway, protein-protein interaction, protein expression, subcellular localization, phosphorylation motif, signaling pathway, protein sequence, blast, molecule, domain, motif, post-translational modification, protein isoform, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEMINI is listed by: re3data.org is related to: Human Proteinpedia is related to: MatrixDB is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: Gene Ontology is related to: Agile Protein Interactomes DataServer has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18988627 PMID:16381900 PMID:14525934 |
Acknowledgement requested, Free, Non-commercial, Commercial requires license | nif-0000-00137, r3d100010978 | https://doi.org/10.17616/R3MK9N | SCR_007027 | Human Protein Reference Database | 2026-02-14 02:05:57 | 1266 | |||||
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ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2026-02-14 02:06:00 | 12 | ||||||
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Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-02-14 02:03:13 | 4 | ||||||||||
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Integrated Manually Extracted Annotation Resource Report Resource Website |
Integrated Manually Extracted Annotation (RRID:SCR_008876) | Integrated MEA, Integrated LinkOut, Manually Extracted Annotation, | data or information resource, database | A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org | biomedical, bibliographic, linkout, literature |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Gene Ontology Tools is related to: BAMS Connectivity is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: BioNumbers is related to: PubMed is related to: Brain Architecture Management System is related to: CellML Model Repository is related to: CHEBI is related to: Comparative Toxicogenomics Database (CTD) is related to: Coriell Cell Repositories is related to: Drug Related Gene Database is related to: DrugBank is related to: Gene Weaver is related to: Internet Brain Volume Database is related to: Cell Centered Database is related to: Brede Database is related to: ModelDB is related to: NeuronDB is related to: NeuroMorpho.Org is related to: Nuclear Receptor Signaling Atlas is related to: Cell Image Library (CIL) is related to: Animal Imaging Database is related to: Olfactory Receptor DataBase is related to: Glomerular Activity Response Archive is related to: CRCNS is related to: OMIM is related to: Rat Genome Database (RGD) is related to: Visiome Platform is related to: NIDA Data Share is related to: bioDBcore is related to: Addgene is related to: Antibody Registry is related to: Beta Cell Biology Consortium is related to: FlyBase is related to: SumsDB is related to: SciCrunch Registry is related to: Mouse Genome Informatics Transgenes is related to: NCBI Taxonomy is related to: OpenNeuro is related to: PeptideAtlas is related to: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat is related to: NIF Registry Automated Crawl Data is related to: AutDB is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: Avian Brain Circuitry Database is related to: Zebrafish Information Network (ZFIN) is related to: GeneDB is related to: WormBase is related to: YPED has parent organization: Integrated |
PMID:20387131 PMID:18975149 |
Data are licensed by their respective owners. Use and distribution is subject to the Terms of Use by the original resource as well as the, Creative Commons Attribution License | nlx_149407 | http://neuinfo.org/nif/nifgwt.html?query=nlx_149407, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_149407-1 | SCR_008876 | Integrated Manually Extracted Annotation View, NIF Integrated LinkOut, NIF Integrated Manually Extracted Annotation, NIF LinkOut | 2026-02-14 02:06:10 | 0 | |||||
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SynaptomeDB Resource Report Resource Website |
SynaptomeDB (RRID:SCR_000157) | SynaptomeDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, protein, pathway, synaptome, protein-protein interaction, synaptic gene, synapse, motif, presynaptic, postsynaptic, vesicle |
is related to: Gene Ontology has parent organization: Johns Hopkins University; Maryland; USA |
PMID:22285564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157656 | SCR_000157 | 2026-02-14 02:05:31 | 0 | |||||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-02-14 02:06:04 | 76 | ||||||
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LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | data or information resource, database | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-02-14 02:06:13 | 3 | ||||
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Integrated Molecular Interaction Database Resource Report Resource Website 1+ mentions |
Integrated Molecular Interaction Database (RRID:SCR_003546) | IMID | data or information resource, database | Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database. | pathway, disease, gene ontology, specie, interaction, molecular, protein-protein interaction, gene/protein regulation, protein-small molecule interaction, gene, protein, regulation |
is related to: Gene Ontology is related to: Entrez Gene is related to: Pathway Commons is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Search Tool for Interactions of Chemicals is related to: KEGG is related to: Pathway Interaction Database is related to: Reactome is related to: PharmGKB has parent organization: Florida State University; Florida; USA |
PMID:22238258 | nlx_157667 | SCR_003546 | 2026-02-14 02:05:44 | 1 | ||||||||
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Cotton EST Database Resource Report Resource Website 10+ mentions |
Cotton EST Database (RRID:SCR_003301) | Cotton EST Database | data or information resource, database | Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information. | expressed sequence tag, contig, indel mutant, single nucleotide polymorphism, transcription factor, protein kinase, gene, mirna, blast, est-simple sequence repeat, simple sequence repeat, pathway, function |
is related to: Gene Ontology is related to: KEGG has parent organization: East Carolina University; Carolina; USA |
PMID:22087239 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011232 | https://doi.org/10.17616/R3X63C | http://www.leonxie.com/ | SCR_003301 | 2026-02-14 02:05:43 | 10 | |||||
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SwissLipids Resource Report Resource Website 10+ mentions |
SwissLipids (RRID:SCR_019074) | data or information resource, database | Expert curated resource that provides framework for integration of lipid and lipidomic data with biological knowledge and models. Provides curated knowledge of lipid structures and metabolism which is used to generate in silico library of feasible lipid structures. These are arranged in hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. Provides reference namespace for lipidomic data publication, data exploration and hypothesis generation. | Lipid, lipidomic data, curated lipid data, lipid structure, lipid metabolism, mass spectrometry analytical output, refernce namespace, lipidomic data publication, hypothesis generation |
uses: UniProt uses: CHEBI uses: RHEA uses: Gene Ontology |
Swiss Federal Government ; SystemsX.ch |
DOI:10.1093/bioinformatics/btv285 | Free, Freely available | r3d100012603 | https://doi.org/10.17616/R3TZ18 | SCR_019074 | 2026-02-14 02:06:49 | 16 | ||||||
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ErmineJ Resource Report Resource Website 50+ mentions |
ErmineJ (RRID:SCR_006450) | ermineJ | software application, data processing software, data analysis software, software resource | Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | microarray, gene ontology, analysis, high-throughput, gene, gene expression, statistical analysis, term enrichment, genome |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of British Columbia; British Columbia; Canada has parent organization: Columbia University; New York; USA |
PMID:16280084 | Free for academic use | nif-0000-07758 | SCR_006450 | ermineJ: Gene Ontology analysis for high-throughput data | 2026-02-15 09:19:16 | 50 | ||||||
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StRAnGER Resource Report Resource Website 10+ mentions |
StRAnGER (RRID:SCR_004247) | StRAnGER | software application, data processing software, data analysis software, software resource | StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER''''s algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. Platform: Online tool | controlled vocabulary, functional analysis, genomics, annotation, visualization, statistical analysis, term enrichment, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Hellenic Research Foundation |
PMID:21293737 | Free for academic use | nlx_25932 | SCR_004247 | Statistical Ranking of ANotated Genomic Experimental Results | 2026-02-15 09:18:43 | 18 | ||||||
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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, data processing software, data analysis software, 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 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-02-15 09:19:58 | 8 | |||||
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GOdist Resource Report Resource Website |
GOdist (RRID:SCR_005770) | GOdist | software application, data processing software, data analysis software, 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 | 2026-02-15 09:19:02 | 0 | |||||||
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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, data processing software, data analysis software, 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 | Tools for High-throughput Experiments Analysis | 2026-02-15 09:19:12 | 0 | |||||
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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | software application, data processing software, data analysis software, 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 | 2026-02-15 09:19:03 | 26 | ||||||
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GOArray Resource Report Resource Website 1+ mentions |
GOArray (RRID:SCR_005785) | GOArray | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:19:03 | 1 | |||||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | web application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-02-15 09:17:57 | 1 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
