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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Extended Alternatively Spliced EST Database Resource Report Resource Website |
Extended Alternatively Spliced EST Database (RRID:SCR_008186) | EASED | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. An online available compendium of alternative splice forms for several organisms (Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Rattus norvegicus, Xenopus laevis). Alternative splice forms are defined by comparing high-scoring ESTs to mRNA sequences (both from GenBank) with known exon-intron information (from ENSEMBL database) using BLAST. Repetitive sequences of all mRNAs have beforehand been masked by MaskerAid. Filtering programs with defined parameters compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which suggest the existence of alternative splice forms. The database is accessible by typing in accession numbers (ACC) or keywords like description, gene names, organism or other keywords. (If more than one hit was found a list of all results is given.) And the result page is divided into 4 major parts. The first part (General Information About The Entry) summarizes the most important information as database ids, organism, and description. The so called alternative splice profile (ASP) of each human sequence is shown in the second part (Alternative Splice Frequency). The ASP indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE corresponds to the EST coverage and can be used as a quality value for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Moreover the number of ESTs from cancerous tissues is shown. The histological source and the developmental stages are illustrated with several colors to enables the user to get an overview of the origins of the matching ESTs. Also, the Splice Site View shows graphically all alternative splice sites for the whole transcript. | drosophila melanogaster, est, exon, filtering, form, gene structure, aligned, alternative, arabidopsis thaliana, bos taurus, caenorhabditis elegans, cancerous, color, danio rerio, deletion, developmental, histological, homo sapien, insertion, intron, mrna, mus musculus, nucleotide sequence, organism, pair, rattus norvegicus, sequence, splice, splice sites databases, stage, tissue, xenopus laevis | has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21138 | SCR_008186 | Extended Alternatively Spliced EST Database | 2025-05-06 11:05:54 | 0 | |||||||
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C. elegans RNAi Collection (Ahringer) Resource Report Resource Website 10+ mentions |
C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) | data or information resource, database | C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies. | Source BioScience Ltd, data, collection, bacterial, strain, Caenorhabditis elegans, RNA, interference, RNAi, gene, function, analysis, feeding, library | has parent organization: University of Cambridge; Cambridge; United Kingdom | Howard Hughes Medical Institute Predoctoral Fellow- ship ; Wellcome Trust Senior Research Fellowship |
PMID:12828945 | Available for purchase | SCR_017064 | 2025-05-06 11:12:25 | 13 | ||||||||
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PhenomicDB Resource Report Resource Website 10+ mentions |
PhenomicDB (RRID:SCR_013051) | PhenomicDB | data or information resource, database | PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher. | phenotype, human, mouse, drosophila, caenorhabditis elegans, dictyostelium discoideum, yeast, zebrafish | PMID:20562418 | nif-0000-03274 | SCR_013051 | 2025-05-06 11:09:00 | 10 | |||||||||
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GeneSpeed- A Database of Unigene Domain Organization Resource Report Resource Website |
GeneSpeed- A Database of Unigene Domain Organization (RRID:SCR_002779) | data or information resource, analysis service resource, service resource, database, production service resource, data analysis service, resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells. | molecular neuroanatomy resource, drosophila melanogaster, genome, caenorhabditis elegans, c. elegans, genomics, homo sapiens, mus musculus, protein domain, transcriptome |
is related to: Gene Ontology is related to: InterPro is related to: Pfam is related to: UniGene has parent organization: University of Colorado Denver; Colorado; USA |
NIDDK P30DK57516; NIDDK DK61248 |
PMID:17132830 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02887 | http://genespeed.uchsc.edu/, http://genespeed.ccf.org | SCR_002779 | GeneSpeed Database | 2025-05-08 10:55:45 | 0 | |||||
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Chemical Effects in Biological Systems (CEBS) Resource Report Resource Website 10+ mentions |
Chemical Effects in Biological Systems (CEBS) (RRID:SCR_006778) | CEBS | storage service resource, data or information resource, service resource, database, data repository | Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency. | caenorhabditis elegans, chemical study, microarray, genetic alteration, toxicogenomics, environmental health, study design, timeline, clinical chemistry, histopathology, proteomics, chemical, clinical, microarray hybridization, gel image, phenotype, pharmacology, toxicology |
is recommended by: National Library of Medicine has parent organization: National Institute of Environmental Health Sciences |
NIGMS ; NIEHS |
PMID:17962311 | Free, Freely available | nif-0000-02649 | SCR_006778 | CEBS, Chemical Effects in Biological Systems (CEBS), Chemical Effects in Biological Systems | 2025-05-08 10:58:15 | 19 | |||||
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GenomeRNAi Resource Report Resource Website 100+ mentions |
GenomeRNAi (RRID:SCR_013088) | storage service resource, data or information resource, service resource, database, data repository | GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome | drosophila genome, caenorhabditis elegans, caenorhabditis elegans genome, c. elegans, drosophila, drosophila cells, human genome, rnai |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: German Cancer Research Center |
nif-0000-02901 | https://www.ncbi.nlm.nih.gov/gap | SCR_013088 | GenomeRNAi, Genome RNAi | 2025-05-08 11:00:21 | 190 | ||||||||
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Model Organisms for Biomedical Research Resource Report Resource Website 10+ mentions |
Model Organisms for Biomedical Research (RRID:SCR_007282) | Model Organisms for Biomedical Research | data or information resource, portal, topical portal | Information about national and international activities and major resources that are being developed to facilitate biomedical research using animal models Mammalian Models: * Mouse * Rat Non-Mammalian Models * S. cerevisiae (budding yeast) * S.pombe (Fission Yeast) * Neurospora (filamentous fungus) * D. discoideum (social amoebae) * C. elegans (round worm) * Daphnia * D. melanogaster (fruit fly) * D. rerio (zebrafish) * Xenopus (frog) * Gallus (chicken) Other Model Organisms: * Arabidopsis | mammal, model organism, mouse, rat, saccharomyces cerevisiae, saccharomyces pombe, neurospora, dictyostelium discoideum, caenorhabditis elegans, daphnia, drosophila melanogaster, zebrafish, xenopus, gallus, arabidopsis, organism supplier | has parent organization: National Institutes of Health | nif-0000-00062 | SCR_007282 | NIH Model Organisms for Biomedical Research, NIH Model Organisms | 2025-05-07 11:51:02 | 11 | ||||||||
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Caenorhabditis Genetics Center Resource Report Resource Website 1000+ mentions |
Caenorhabditis Genetics Center (RRID:SCR_007341) | CGC | organism supplier, biomaterial supply resource, material resource, cell repository | Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available. | non-human animal, caenorhabditis elegans, chromosome, database, model, mutant, nematode, nomenclature, model organism, protein, transgenic, web accessible database, genetic stock, germplasm, genotype, FASEB list |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: C. elegans Gene Knockout Consortium is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIH OD010440 | nif-0000-00240 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models http://www.cbs.umn.edu/research/resources/cgc |
http://biosci.umn.edu/CGC/, http://www.cgc.cbs.umn.edu | SCR_007341 | 2025-05-08 10:58:42 | 2849 | ||||||
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NIA Scientific Resources Resource Report Resource Website |
NIA Scientific Resources (RRID:SCR_008269) | NIA Scientific Resources | organism supplier, biomaterial supply resource, material resource | A resource that provides information on the vast number of resources available from the National Institute of Aging. NIA maintains approximately 150 primates (Macaca mulatta) at four regional primate centers where aging-related research is conducted. NIA also maintains colonies of aged rats and mice that are used for age-related disease research. This resource supports a multi-institutional study, the Interventions Testing Program (ITP), that investigates diets and dietary supplements that extend lifespan, delay disease and avoid dysfunction. NIA is also in charge of a microarray facility which provides filter arrays of 17,000 mouse cDNA clone sets that were developed at the NIA Intramural Research Program Laboratory of Genetics. NIA supports studies that provide biospecimens that can be shared for later research. This resource also helps the C. elegans Genetic Center at the University of Minnesota, which contains 1,000 strains of C. elegans that can be used for aging studies. This resource also provides a searchable database for epidemiological research on aging. There is access to social and behavioral research materials, including books on aging and health, from the research was conducted and supported by NIA. There are links to federal web sites that are further resources for aging research that were supported by NIA. | macaca mulatta, rodent, epidemiological, fibroblast, genetics, alzheimer's disease, animal, array, behavioral, caenorhabditis elegans, cdna, cell, colony, culture, disease, dna, human, hutchinson-guilford, intervention, microarray, mouse, mutation, non-human primate, premature, primate, progeria, rat, repository, scientific, skin, social, supplement, syndrome, werner, diet, dietary supplement, longitudinal, health |
has parent organization: National Institute on Aging is parent organization of: NIA Aged Rodent Colonies is parent organization of: NIA Nonhuman Primate Tissue Bank is parent organization of: NIA Mutant Mouse Aging Colony Handbook is parent organization of: Database for Sharing Aging Research Models is parent organization of: Aged Rodent Tissue Bank |
Aging | NIA | nif-0000-23759 | http://www.nia.nih.gov/ResearchInformation/ScientificResources/ | SCR_008269 | NIA Non-Human Primate Centers and Tissue Banks | 2025-05-08 10:59:04 | 0 | |||||
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NIH Neuroscience Microarray Consortium Resource Report Resource Website 1+ mentions |
NIH Neuroscience Microarray Consortium (RRID:SCR_004930) | storage service resource, data or information resource, analysis service resource, service resource, database, production service resource, data analysis service, data repository | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis. | arabidopsis, bos taurus, chicken, caenorhabditis elegans, drosophila, human, rhesus monkey, mouse, rat, songbird, xenopus, yeast, zebra finch |
is used by: NIF Data Federation is related to: Songbird Brain Transcriptome Database has parent organization: National Institutes of Health |
NIH Blueprint for Neuroscience Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00074 | http://arrayconsortium.tgen.org, http://np2.ctrl.ucla.edu/np2/home.do | SCR_004930 | NIH Neuroscience Microarray Consortium | 2025-05-08 10:57:15 | 4 | ||||||
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Expression Patterns for C. elegans promoter GFP fusions Resource Report Resource Website 1+ mentions |
Expression Patterns for C. elegans promoter GFP fusions (RRID:SCR_001619) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format. | expression, gene, gene expression, caenorhabditis elegans, c. elegans, genomic, green fluorescent protein, location, locus, pattern, stage, strain, tissue |
is listed by: One Mind Biospecimen Bank Listing is related to: WormAtlas is related to: WormBase is related to: Caenorhabditis Genetics Center is related to: NEXTDB has parent organization: Albert Einstein College of Medicine; New York; USA |
Genome Canada ; Genome British Columbia |
PMID:17850180 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153885, nif-0000-25220, SCR_008354 | SCR_001619 | Caenorhabditis elegans Expression Patterns | 2025-05-07 11:47:11 | 4 | ||||||
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Caenorhabditis elegans Natural Diversity Resource (CeNDR) Resource Report Resource Website 10+ mentions |
Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) | CeNDR | organism supplier, biomaterial supply resource, material resource | Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery. | c. elegans, caenorhabditis elegans, strains, n2, roundworm, nematode, gene analysis, organism supplier, portal | has parent organization: Northwestern University; Illinois; USA | American Cancer Society Research Scholar Award ; Amazon Web Services Research Grant ; Weinberg College of Arts and Sciences starter innovation award ; Northwestern University Start-up Funds ; NIGMS R01GM107227; NSF DGE-1324585 |
PMID:27701074 | Available to the research community | SCR_014958 | Caenorhabditis elegans Natural Diversity Resource | 2025-05-08 11:01:10 | 22 |
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