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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | software resource, data processing software, software application, 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 | 2026-08-05 10:44:20 | 26 | ||||||
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GOArray Resource Report Resource Website 1+ mentions |
GOArray (RRID:SCR_005785) | GOArray | software resource, data processing software, software application, 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 | 2026-08-05 10:44:20 | 1 | |||||||
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mirEX Resource Report Resource Website 10+ mentions |
mirEX (RRID:SCR_006060) | mirEX | data or information resource, database, atlas, data analysis service, production service resource, service resource, analysis service resource | mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window. | microrna gene expression, microrna, gene expression, gene, organ, developmental stage, plant, seed, seedling, mature plant, pri-mirna, biotic stress, abiotic stress, organ formation, primer, cdna | has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland | Foundation for Polish Science ; European Union ; Regional Development Fund MPD 2010/3; Polish Ministry of Science and Higher Education 3011/B/P01/2009/37 |
PMID:22013167 | nlx_151462 | http://bioinfo.amu.edu.pl/mirex | SCR_006060 | 2026-08-05 10:44:25 | 10 | ||||||
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Brain Test Resource Report Resource Website |
Brain Test (RRID:SCR_006212) | Brain Test | data or information resource, topical portal, portal | A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help. | neuropsychiatry, brain, behavior, behavioral assessment, questionnaire, cognitive test, crowdsourcing, online study, memory, attention, brain disease, gene, exercise, genetics, mental disease, mental health, research project, research | has parent organization: University of California at Los Angeles; California; USA | Attention deficit-hyperactivity disorder, Schizophrenia, Bipolar Disorder, Mental disease, Normal, Autism Spectrum Disorder | NIMH ; NARSAD |
nlx_151777 | SCR_006212 | Brain Test project | 2026-08-05 10:44:24 | 0 | ||||||
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GWAS Central Resource Report Resource Website 100+ mentions |
GWAS Central (RRID:SCR_006170) | data or information resource, data repository, database, storage service resource, service resource | Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P. | Human Genome Variation database of Genotype-to-Phenotype information, genetic association study, genotype, phenotype, gene, genome region, disease, frequency data, region, genome, marker, single nucleotide polymorphism, genetic variant, allele, genome wide association study, human genome, chromosome, genetics |
is listed by: re3data.org is related to: dbSNP has parent organization: University of Leicester; Leicester; United Kingdom |
European Union GEN2PHEN project ; University of Leicester; Leicester; United Kingdom ; GlaxoSmithKline |
PMID:18948288 | nlx_151672, nif-0000-02958, SCR_007709, r3d100010565 | http://www.hgvbaseg2p.org, https://doi.org/10.17616/R34G8W | SCR_006170 | Genome Wide Association Studies Central, Human Genome Variation database of Genotype to Phenotype information, HGVbaseG2P | 2026-08-05 10:44:27 | 105 | ||||||
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Research Accelerator Resource Report Resource Website 1+ mentions |
Research Accelerator (RRID:SCR_006051) | UCSD Research Accelerator | data or information resource, portal, community building portal, database, service resource | Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity. | collaboration, transdisciplinary research, gene, pathway, disease, cell line, data, human sample, laboratory protocol, medical device, equipment, resource, reagent, research project, transgenic animal, knock out animal, validated antibody, yale keck proteomics assay, allergy, immunology, bone, joint, orthopedic, cancer, cardiovascular, gastroenterology, infectious disease, neurologic disease, organ transplantation, psychiatric disease, reproductive disease, vascular disease, sharing, material resource |
is used by: University College London; London; United Kingdom is used by: University of Cambridge; Cambridge; United Kingdom is used by: Washington University in St. Louis; Missouri; USA is used by: University of Chicago; Illinois; USA is used by: University of Pennsylvania; Philadelphia; USA is used by: Yale University; Connecticut; USA has parent organization: University of California at San Diego; California; USA |
Allergy, Immunology, Bone, Joint, Orthopedic, Cancer, Cardiovascular, Gastroenterology, Infectious Disease, Neurologic disease, Organ Transplantation, Psychiatric disease, Reproductive disease, Vascular disease | The community can contribute to this resource | nlx_151451 | SCR_006051 | ResearchAccelerator.org, ResearchAccelerator | 2026-08-05 10:44:25 | 1 | ||||||
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UMD-BRCA1/ BRCA2 databases Resource Report Resource Website 10+ mentions |
UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) | UMD-BRCA1/ BRCA2 databases | data or information resource, data repository, database, storage service resource, service resource | The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau. | cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, woman, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Health and Medical Research; Rennes; France |
Breast cancer, Ovarian cancer | French National Cancer Institute ; European Union FP7/2007-2013; Association dAide a la Recherche Cancerologique de Saint Cloud |
PMID:22144684 | The UMD- BRCA1 Locus Specific Databases constitute the intellectual property of the curators of the database. Any unauthorized copying, Storage or distribution of this material without written permission from the curators would lead to copyright infringement with possible ensuing litigation. | nlx_151608, biotools:brca_share | https://bio.tools/brca_share | SCR_006128 | UMD-BRCA1 mutations database, UMD-BRCA1 / BRCA2 databases, UMD-BRCA1/BRCA2 databases | 2026-08-05 10:44:23 | 26 | |||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | software resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:44:27 | 35 | |||||||
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OGEE - Online GEne Essentiality database Resource Report Resource Website 1+ mentions |
OGEE - Online GEne Essentiality database (RRID:SCR_006080) | OGEE, OGEEdb | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart. | genome-wide association study, essentiality, gene, essential gene, non-essential gene, growth, expression profile, duplication status, conservation, evolutionary origin, embryonic development, text-mining, gene function, environment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
BMBF 0315450C | PMID:22075992 | Free | nlx_151488, biotools:ogee | https://bio.tools/ogee | SCR_006080 | Online GEne Essentiality database | 2026-08-05 10:44:25 | 2 | ||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-08-05 10:44:22 | 77 | |||||
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CREATE Resource Report Resource Website 50+ mentions |
CREATE (RRID:SCR_006133) | CREATE | data or information resource, narrative resource, portal, international standard specification, topical portal, database, standard specification | The CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO). | cre driver, mutagenesis, cre, gene, allele, mutant mouse es cell line, mutant mouse, es cell line, phenotype, gene expression, cre recombinase, tissue, organ, cell, mouse mutagenesis, cre line, FASEB list |
is related to: Recombinase (cre) Activity has parent organization: European Bioinformatics Institute is parent organization of: CreZOO |
European Union FP7 HEALTH-2007-2.1.2-6; European Union FP7 223487 |
PMID:21195764 | nlx_151617 | SCR_006133 | CREATE (Coordination of resources for conditional expression of mutated mouse alleles) project, CREATE - Coordination of resources for conditional expression of mutated mouse alleles, CREATE portal, CREATE (Coordination of resources for conditional expression of mutated mouse alleles) | 2026-08-05 10:44:26 | 50 | ||||||
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phenomeNET Resource Report Resource Website 10+ mentions |
phenomeNET (RRID:SCR_006165) | PhenomeNet | data or information resource, source code, database, software resource, data analysis service, production service resource, service resource, analysis service resource | PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing | phenotype, disease, gene, genotype, allele, model organism, human disease, candidate disease gene, pathway, orthologous gene, ortholog, ontology, semantic similarity, mutant phenotype, disease pathway, alignment, pharmacogenomics, drug |
is related to: OMIM is related to: Orphanet is related to: PharmGKB is related to: MPO has parent organization: University of Cambridge; Cambridge; United Kingdom |
European Union 7th FPRICORDO project 248502; NHGRI R01 HG004838-02; BBSRC BBG0043581 |
PMID:21737429 | The source code and all data are freely available on http://phenomeblast.googlecode.com | nlx_151667 | SCR_006165 | PhenomeNet - Cross Species Phenotype Network | 2026-08-05 10:44:23 | 13 | |||||
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Phenexplorer Resource Report Resource Website 1+ mentions |
Phenexplorer (RRID:SCR_006156) | PhenExplorer | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | The PhenExplorer allows you to browse the Human Phenotype Ontology (HPO) in different ways, using the tabs ''''by features'''', ''''by disease'''', ''''by ontology'''' or ''''by genes''''. Clicking on a particular phenotypic feature (HPO-term) you can get a list of disease entries that are linked to it (i.e. diseases that are annotated with this HPO-term). You can also visualize this term in the context of the ontological structure. Finally, a lists of genes can be displayed, that are known to cause (when mutated) the linked diseases mentioned above. For each disease you can get the list of linked HPO-terms and genes. You can also search for specific genes and explore to which HPO-terms and diseases they are linked. | phenotype, ontology, feature, disease, gene |
is used by: Human Phenotype Ontology is related to: Human Phenotype Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
nlx_151656 | SCR_006156 | PhenExplorer - Explore the Human Phenotype Ontology | 2026-08-05 10:44:27 | 2 | ||||||||
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Gene-Disease Association Type Ontology Resource Report Resource Website |
Gene-Disease Association Type Ontology (RRID:SCR_006159) | data or information resource, ontology, controlled vocabulary | Ontology that describes the different types of associations between a gene and a disease. It was developed to integrate information from different databases that contain gene-disease associations such as UniProt, CTD, Orphanet, the GWAS Catalog, GAD, MGD, RGD, and LHGDN. | gene, disease, owl, ontology |
is affiliated with: DisGeNET has parent organization: Pompeu Fabra University; Barcelona; Spain |
PMID:21695124 PMID:24602174 |
Free | nlx_151711 | http://www.disgenet.org/web/DisGeNET/menu/downloads | SCR_006159 | Gene Disease Association, GeneDiseaseAssociation Type Ontology | 2026-08-05 10:44:26 | 0 | ||||||
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Hereditary Hearing Loss Homepage Resource Report Resource Website 100+ mentions |
Hereditary Hearing Loss Homepage (RRID:SCR_006469) | Hereditary Hearing Loss | data or information resource, portal, topical portal, database, atlas | Overview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site. | cochlea, syndromic, nonsyndromic, gene, genetics, hearing impairment, hearing, ear, FASEB list |
is listed by: OMICtools is related to: MITOMAP - A human mitochondrial genome database has parent organization: University of Iowa; Iowa; USA has parent organization: University of Antwerp; Antwerp; Belgium |
Hereditary hearing impairment, Hearing impairment | nif-0000-00075, OMICS_01542 | SCR_006469 | 2026-08-05 10:44:29 | 455 | ||||||||
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ErmineJ Resource Report Resource Website 50+ mentions |
ErmineJ (RRID:SCR_006450) | ermineJ | software resource, data processing software, software application, data analysis software | 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 | 2026-08-05 10:44:29 | 50 | ||||||
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Genes Cognition and Psychosis Program Resource Report Resource Website 1+ mentions |
Genes Cognition and Psychosis Program (RRID:SCR_006292) | GCAP | data or information resource, topical portal, portal, disease-related portal | Schizophrenia related portal that aims to solve the mystery of genetic predisposition to psychosis, develop new methods for early diagnosis and prevention, and discover new treatments that will cure people suffering from it. Our objectives are to fully characterize: # neurobiological mechanisms related to susceptibility genes for schizophrenia and related clinical disorders; # genetic variation in aspects of cognition and emotionality associated with schizophrenia; and # small molecular targets for novel therapies. A unique feature of this Program is that its diverse scientific resources will be focused on a highly specific scientific agenda, that is to acquire the critical biological information about the susceptibility genes associated with schizophrenia and related illnesses. Our mission and goal, to understand the basic mechanisms of serious mental illness, has again guided us into new areas of research and to new insights. We have found evidence of new genes implicated in the cause of schizophrenia and involved in brain functions related to cognition and emotion and we have begun to explore how genes interact with each other and with the environment to individualize risk for these conditions. We are working now with over 20 genes related to schizophrenia. One of the key developments in our research over the past year has been the emergence of some targets for the development of novel therapeutics. We have discovered a new schizophrenia susceptibility gene, KCNH2, which represents the first clear target for the development of novel treatments. Just in this past year, for example, we published the first extensive statistical analysis of how schizophrenia genes may vary in their risk effects based on different genetic background (Nicodemus et al Hum Gen 2006), the first studies of schizophrenia genes interacting in effecting gene expression in brain (Lipska et al Hum Mol Genetics 2006a, Lipska et al Hum Mol Gen 2006 b); the first evidence that the mechanism of genetic association of NRG1 with schizophrenia involves a novel isoform of the gene in human brain (Law et al PNAS 2006), and the first evidence that MAOA may be linked to mood and impulse control because it effects critical mood regulatory neural networks (Meyer-Lindenberg et al PNAS 2006). | gene, genetic variation, cognition, emotion, therapeutics, treatment, drug development, brain function, psychosis, drug |
is related to: NIMH Intramural Research Program Clinical Brain Disorders Branch has parent organization: NIMH Division of Intramural Research Programs |
Schizophrenia, Mental illness, Psychiatric disorder | NIMH | nlx_151948 | SCR_006292 | 2026-08-05 10:44:27 | 1 | |||||||
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COLT-Cancer Resource Report Resource Website 10+ mentions |
COLT-Cancer (RRID:SCR_006485) | COLT-Cancer | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | The COLT-Cancer database is a collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using the microarray detection platform developed in the COLT (CCBR-OICR Lentiviral Technology) facility at the Moffat Lab. All shRNA dropout profiles are freely available through download or queries via this website. | gene, shrna profile, shrna, functional genetics, cancer, cell line, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Toronto; Ontario; Canada |
Pancreatic cancer, Ovarian cancer, Breast cancer | Ontario Institute for Cancer Research ; Terry Fox Research Institute ; Canadian Institutes of Health Research ; Canada Foundation for Innovation ; Ontario Research Fund |
PMID:22102578 | Free | biotools:colt-cancer, nlx_149426 | https://bio.tools/colt-cancer | SCR_006485 | CCBR-OICR Lentiviral Technology Cancer, COLT-Cancer database | 2026-08-05 10:44:29 | 11 | |||
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European Nucleotide Archive (ENA) Resource Report Resource Website 1000+ mentions |
European Nucleotide Archive (ENA) (RRID:SCR_006515) | ENA | data or information resource, data repository, database, storage service resource, service resource | Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource. | analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standard |
is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: NCBI Sequence Read Archive (SRA) is related to: ENA Sequence Version Archive is related to: VBASE2 is related to: DDBJ Sequence Read Archive is related to: ISA Infrastructure for Managing Experimental Metadata is related to: DNA DataBank of Japan (DDBJ) is related to: DNA DataBank of Japan (DDBJ) is related to: NCBI is related to: INSDC is related to: INSDC is related to: NCBI Assembly Archive Viewer has parent organization: European Bioinformatics Institute is parent organization of: ENA Sequence Search works with: Eutherian comparative genomic analysis protocol |
EMBL ; Wellcome Trust ; European Union |
PMID:20972220 | Public, The community can contribute to this resource, Acknowledgement requested | OMICS_01029, r3d100010527, nif-0000-32981 | http://www.ebi.ac.uk/embl/, https://doi.org/10.17616/R3HW3J | SCR_006515 | ENA, European Nucleotide Archive | 2026-08-05 10:44:29 | 1272 | ||||
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Comparative Toxicogenomics Database (CTD) Resource Report Resource Website 1000+ mentions |
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) | CTD | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks. | environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browser, FASEB list |
is used by: DisGeNET is used by: NIF Data Federation is listed by: 3DVC is listed by: Gene Ontology Tools is related to: PharmGKB Ontology is related to: Gene Ontology is related to: BioRAT is related to: Integrated Gene-Disease Interaction is related to: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Mount Desert Island Biological Laboratory has parent organization: North Carolina State University; North Carolina; USA is parent organization of: Interaction Ontology |
Pfizer ; American Chemistry Council ; NIEHS ES014065; NIEHS R01 ES019604; NCRR P20 RR016463; NIEHS U24 ES033155 |
PMID:16902965 PMID:16675512 PMID:14735110 PMID:12760826 |
Free, Freely available | OMICS_01578, nif-0000-02683, r3d100011530 | http://ctd.mdibl.org, https://doi.org/10.17616/R3KS7N | SCR_006530 | CTD - Comparative Toxicogenomics Database | 2026-08-05 10:44:30 | 1188 |
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