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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-07-25 12:07:05 | 37 | ||||||
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Spliceman Resource Report Resource Website 1+ mentions |
Spliceman (RRID:SCR_005354) | Spliceman | analysis service resource, service resource, data analysis service, production service resource | An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish. | dna sequence, pre-mrna, splicing, pre-mrna splicing, point mutation, mutation, sequence variation, fasta |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:22328782 | Free, Non-commercial, Commercial use requires license | OMICS_02259 | SCR_005354 | 2026-07-27 09:32:15 | 5 | |||||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-07-27 09:31:33 | 11 | ||||
|
RAVEN Resource Report Resource Website 100+ mentions |
RAVEN (RRID:SCR_001937) | RAVEN | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor binding site, phylogenetic footprint, regulatory sequence variation, genetic variation, in silico, regulatory sequence, FASEB list |
uses: Embassy-domsearch is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
PMID:18208319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01932 | SCR_001937 | Regulatory analysis of Variation in Enhancers, RAVEN - Regulatory analysis of Variation in ENhancers | 2026-07-28 09:40:28 | 127 | ||||||
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CRISPRdirect Resource Report Resource Website 100+ mentions |
CRISPRdirect (RRID:SCR_018186) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-07-28 09:44:51 | 452 | ||||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-07-28 09:40:48 | 4282 | |||||
|
Animal QTLdb Resource Report Resource Website 50+ mentions |
Animal QTLdb (RRID:SCR_001748) | Animal QTLdb | service resource, data or information resource, data repository, database, storage service resource | Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. | chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype |
uses: Entrez Gene uses: Ensembl is used by: NIF Data Federation is used by: MONARCH Initiative is listed by: re3data.org is related to: Ensembl Variation is related to: Vertebrate Trait Ontology has parent organization: Iowa State University; Iowa; USA has parent organization: NAGRP Bioinformatics Coordination Program |
USDA NRSP-8; USDA 2007-04187 |
PMID:23180796 PMID:17245610 |
Free, Freely available | nif-0000-02550, r3d100010744 | http://www.animalgenome.org/QTLdb/ | SCR_001748 | Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database | 2026-07-28 09:40:24 | 50 | ||||
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Ensembl Variation Resource Report Resource Website 1+ mentions |
Ensembl Variation (RRID:SCR_001630) | Ensembl Variation | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population. | genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited disease |
is used by: MONARCH Initiative is related to: dbSNP is related to: Database of Genomic Variants Archive (DGVa) is related to: PubMed is related to: Animal QTLdb is related to: OMIA - Online Mendelian Inheritance in Animals has parent organization: Ensembl |
PMID:23203987 PMID:20562413 PMID:20459810 PMID:20459805 |
Free, Available for download, Freely available | nlx_153897 | SCR_001630 | ensembl variation | 2026-07-28 09:40:14 | 4 | ||||||
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Ancora Resource Report Resource Website 10+ mentions |
Ancora (RRID:SCR_001623) | Ancora | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements. | genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancer |
is related to: MONARCH Initiative has parent organization: University of Bergen; Bergen; Norway |
Research Council of Norway ; Bergen Research Foundation ; Sars Centre |
PMID:18279518 | Free, Freely available | nlx_153891 | SCR_001623 | Atlas of Noncoding Conserved Regions in Animals | 2026-07-28 09:40:20 | 19 | |||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-07-28 09:41:40 | 186 | ||||
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miRNAMap Resource Report Resource Website 100+ mentions |
miRNAMap (RRID:SCR_003156) | miRNAMap | data or information resource, database | A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA. | microrna, genome, FASEB list |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:18029362 PMID:16381831 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03138, OMICS_00408 | SCR_003156 | 2026-07-28 09:40:38 | 246 | |||||||
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PolyA DB Resource Report Resource Website 100+ mentions |
PolyA DB (RRID:SCR_007867) | PolyA_DB | data or information resource, database | A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites. | FASEB list | has parent organization: University of Medicine and Dentistry of New Jersey; New Jersey; USA | SCR_007867 | 2026-07-28 09:41:55 | 101 | ||||||||||
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Aves Labs Resource Report Resource Website 10+ mentions |
Aves Labs (RRID:SCR_001136) | commercial organization | An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing. | antibody, high affinity, chicken antibody, chicken igy, immunoreagents, biomedical, research, immunoglobulin | nlx_152287 | SCR_001136 | 2026-07-25 12:04:55 | 23 | |||||||||||
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FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | FunctSNP - Linking SNPs to functional knowledge | 2026-07-25 12:04:43 | 0 | ||||||
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One Mind Biospecimen Bank Listing Resource Report Resource Website |
One Mind Biospecimen Bank Listing (RRID:SCR_004193) | One Mind Biobanks, One Mind Biobank | cell repository, biomaterial supply resource, material resource | International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly. | biorepository, bio-repository, database, registry, biobank, biospecimen, repository |
is used by: NIF Data Federation is used by: Aging Portal lists: Midwest Transplant Network lists: Danish Multiple Sclerosis Biobank lists: Genetics of Kidneys in Diabetes lists: TEDDY lists: BioEden Tooth Cell Bank lists: Windber Tissue Bank lists: Boston University Alzheimer's Disease Center Neuropathology Core Facility lists: UCL Biobank lists: LifeLegacy Foundation lists: CCLG Tissue Bank lists: ADA GENNID Study lists: Ohio State Leukemia Tissue Bank lists: Feinstein Biorepository lists: Iowa Donor Network lists: National Disease Research Interchange lists: Emory ADRC Tissue and Biospecimen Banking Facility lists: Zebrafish Brain Atlas lists: KI Biobank - Amphetamine dependence lists: KI Biobank - PAIN lists: PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden lists: Africa Centre Biobank lists: UCSF Brain Tumor Tissue Bank lists: Southampton Tumour Bank lists: California National Primate Research Center Analytical and Resource Core lists: CPCTR: Cooperative Prostate Cancer Tissue Resource lists: DIAN - Dominantly Inherited Alzheimer Network lists: ZCre lists: Mexican Health and Aging Study lists: NIDDK Inflammatory Bowel Disease Genetics Consortium lists: Acute Liver Failure Study Group lists: Diabetes Prevention Type 1 lists: NIA Mouse cDNA Project Home Page lists: Type 1 Diabetes Resource lists: BARI 2D lists: Childhood Liver Disease Research and Education Network lists: EuMMCR lists: Living Biobank lists: Nonalcoholic Steatohepatitis Clinical Research Network lists: Drug-Induced Liver Injury Network lists: HALT-C Trial lists: SEARCH for Diabetes in Youth lists: Viral Resistance to Antiviral Therapy of Chronic Hepatitis C lists: GenitoUrinary Development Molecular Anatomy Project lists: Medical Therapy of Prostatic Symptoms lists: Type 1 Diabetes Genetics Consortium lists: Texas A and M Institute for Genomic Medicine lists: Expression Patterns for C. elegans promoter GFP fusions lists: ATCC lists: Genes to Cognition - Biological Resources lists: TCAG lists: World Federation for Culture Collections lists: Italian Rett Syndrome database lists: Addgene lists: Rat Resource and Research Center lists: National Center for Marine Algae and Microbiota lists: UD Chick EST Project lists: NCI Mouse Repository lists: CGSC lists: International Gene Trap Consortium lists: Honey Bee Brain EST Project lists: Marine Biological Laboratory lists: NBRC lists: FANTOM DB lists: UMMC Center for Psychiatric Neuroscience Labs and Facilities lists: Gene Expression Nervous System Atlas lists: Washington National Primate Research Center lists: Primate Embryo Gene Expression Resource lists: Peromyscus Genetic Stock Center lists: Islet Cell Resource Centers lists: National Natural Toxins Research Center lists: GenomEUtwin lists: Drosophila Genomics Resource Center lists: Human Tissue and Organ for Research Resource (HTORR) lists: Special Mouse Strains Resource lists: New England National Primate Research Center lists: Addiction Research GPCR Assay Bank lists: Mutant Mouse Resource and Research Center lists: Penn Induced Pluripotent Stem Cell Core Facility lists: neuromice lists: EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis lists: ShARM lists: NIH NeuroBioBank lists: NIH Human Pluripotent Stem Cell Registry lists: Phoenix lists: The Cancer Genome Atlas lists: MUGEN Mouse Database lists: Coriell Cell Repositories lists: RIKEN BioResource Center lists: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders lists: Retinal Degeneration Rat Model Resource lists: Harvard Brain Tissue Resource Center lists: Glioma Molecular Dignostic Initiatives lists: Source BioScience LifeSciences lists: National Mesothelioma Virtual Bank lists: SpecimenCentral.com lists: Arizona Cancer Center Tumor Bank lists: Cryogenic Laboratories, Inc lists: Partners HealthCare Biorepository lists: National Neurological AIDS Bank lists: Mount Sinai Allograft Technologies lists: EuroBioBank lists: NICHD Brain and Tissue Bank for Developmental Disorders lists: Roswell Park Data Bank and BioRepository lists: Hungarian Neurological-Psychiatric Biobank lists: Roslin Cells lists: Vitiligo Biobank lists: NAF Ataxia Tissue Donation lists: HipSci lists: Cellartis lists: KaLy-Cell lists: Lions Eye Institute for Transplant and Research lists: Endocells lists: Leibniz Institute for Prevention Research and Epidemiology Biobank lists: DCI Tissue and Blood Procurement Shared Resource lists: Childhood Leukaemia Cell Bank lists: Cleveland Clinic Genomic Medicine Biorepository lists: Sunnybrook Tumour Bank lists: Massachusetts Human Stem Cell Bank lists: Liverpool Tissue Bank lists: Dr. Donald MacLellan Tissue Bank lists: OneLegacy lists: Arizona Biospecimen Locator lists: ProMPT - Prostate Cancer Mechanisms of Progression and Treatment lists: British Columbia Gynaecologic Tissue Bank lists: Guthy-Jackson Repository for Neuromyelitis Optica lists: Biorepository Alliance of Georgia for Oncology lists: ITOR Biorepository Services lists: Canadian Tumour Repository Network lists: Progeria Cell and Tissue Bank lists: Wright Medical Technology, Inc. lists: Accelerated Cure Project MS Repository lists: Integrated Biobank of Luxembourg lists: International Biologics, LLC lists: Canadian Breast Cancer Foundation Tumor Bank lists: AIDS and Cancer Specimen Resource lists: Canadian Virtual Brain Tumour Bank lists: UAB Comprehensive Cancer Center Tissue Procurement Shared Facility lists: Cancer Research Network of the FRSQ lists: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) lists: Bangalore Brain Bank lists: Roslin Wellcome Trust Tick Cell Biobank lists: Osiris Therapeutics lists: LifePoint, Inc. lists: American Donor Services lists: Life Alaska Donor Services, Inc. lists: Biobank Graz lists: UCSF DNA Bank lists: Store-a-Tooth Stem Cell Bank lists: UC San Diego Biorepository lists: START Tumor Bank lists: Donor Alliance lists: University of Minnesota Tissue Procurement Facility lists: NEALS Sample Repository lists: South Texas Blood and Tissue Center lists: New Life Generation, Inc. lists: Transplant Services Center lists: Nevada Donor Network, Inc. lists: OECI - Tubafrost: The European Human Frozen Tissue Bank lists: Cincinnati Biobank Core Facility lists: OHSU Biolibrary lists: Ochsner Blood Bank lists: Brown University Rhode Island Biobank Core Facility lists: Myeloma Tissue Bank lists: US Biomax lists: LifeShare Transplant lists: BioStorage Technologies lists: Duke Biobank lists: UAB Alzheimer's Disease Center lists: Duke Biospecimen Repository lists: Center for Organ Recovery and Education - CORE lists: ReproTech, Ltd. lists: Ludwig Boltzman Tumour Bank lists: Lifesharing Tissue Services lists: Donor Network of Arizona lists: Wales Cancer Bank lists: M2Gen Biorepository lists: Medical College of Georgia Tumor Bank lists: Cellular Technology Ltd Cryopreserved PBMC lists: onCore UK lists: Doheny Eye and Tissue Transplant Bank lists: Dana Farber Tissue Bank lists: Karolisnka Biobank lists: Rocky Mountain MS Center Tissue Bank lists: Marshfield Clinic Biobank lists: Mantle Cell Lymphoma Cell Bank lists: Neuroendocrine Tumors Biobank lists: Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility lists: Maryland Brain Collection lists: Angioma Alliance DNA/Tissue Bank and Patient Registry lists: Wisconsin International Stem Cell Bank lists: Mid-America Transplant Services lists: Autism Genetic Resource Exchange lists: Moffitt Cancer Center Tissue Core lists: PROCURE Quebec Prostate Cancer Biobank lists: AIDS Malignancy Bank lists: University of Chicago Human Tissue Resource Center Biospecimen Banking lists: UAB SPORE Biorepository Banks lists: Bone Bank Allografts lists: Allograft Innovations, LLC lists: Origene China lists: Louisiana Organ Procurement Agency - LOPA lists: EDAR study: biomarkers for Alzheimer's disease lists: Cooperative Human Tissue Network lists: UMass Cancer Center Tissue and Tumor Bank lists: Crimson Biospecimen Core lists: ScienceCare lists: St. James Hospital Cryobiology Laboratory Stem Cell Facility lists: BrainNet Europe lists: Essential Tremor Centralized Brain Repository lists: South Dakota Lions Eye Bank lists: Estonian Genome Center lists: Cureline Biopathology lists: Stem-Health Hellas Stem Cell Bank lists: LifeTek OrthoBiologics lists: TissueNet lists: Swedish Regional Biobank lists: Cryo-Save lists: National Surgical Adjuvant Breast and Bowel Project Tissue Bank lists: University of Virginia Tissue Culture Facility lists: KORA-gen lists: Swiss Biobank lists: NIGMS Human Genetic Cell Repository lists: NINDS Repository lists: eyeGENE lists: NHGRI Sample Repository for Human Genetic Research lists: Biobank of Hospital Clinic - IDIBAPS lists: Regional Biobank of Central Norway lists: SeraCare Lifesciences: Sample Storage Management and Processing Services lists: NEI-AREDS Genetic Repository lists: COHORT Repository lists: JP McCarthy Cord Stem Cell Bank lists: Michigan Neonatal Biobank lists: SepNet Central Sample Bank lists: LifeLink Tissue Bank lists: SPH Biorepository lists: Cardio-Facio-Cutaneous Syndrome International Biobank lists: DCI Donor Services lists: LifeGift Organ Donation Center lists: Inflammatory Breast Cancer Biobank lists: University of Miami Tissue Bank lists: LifeNet Health of Florida lists: UTHealth BioBank lists: Southwest France Tumour Bank lists: Southern Alberta Organ and Tissue Donation Program lists: Blood and Tissue Center of Central Texas lists: MD Anderson Clone Bank lists: Community Tissue Services - CTS lists: Aurora Healthcare Biorepository lists: Human Biological Data Interchange lists: Bio-Options lists: Cancer Center Tissue Bank - Fudan University lists: British Columbia Tumour Tissue Repository lists: BioReliance Biorepository lists: New York Firefighters Skin Bank lists: GSDS - Golden State Donor Services lists: UK Multiple Sclerosis Tissue Bank lists: UCL/UCLH Biobank for Studying Health and Disease lists: Tumorbank Bern lists: IPBIR - Integrated Primate Biomaterials and Information Resource lists: Stanford Tissue Bank lists: HD Community BioRepository lists: Autism Research Resource lists: Yerkes Collection Non-Human Primate Resource lists: Hollings Cancer Center Tissue Biorepository and Research Pathology Services Shared Resource lists: Washington Regional Transplant Community - WRTC lists: Vanderbilt BioVU lists: Jackson Laboratory lists: Central England Haemato-Oncology Research Biobank lists: Genethon DNA and Cell Bank lists: University of Michigan Biorepository lists: Simons Simplex Collection lists: Gift of Life Donor Program lists: Queen Square Brain Bank lists: SeqWright Biorepository lists: Telethon Network of Genetic Biobanks lists: New York Organ Donor Network - NYODN lists: Wistar Institute Collection at Coriell lists: USIDNET DNA and Cell Repository lists: Brain Bank for Autism lists: Living Legacy Foundation of Maryland lists: Beaumont Hospitals Biobank lists: Central Biomaterial Bank - German Heart Failure Network lists: PXE International Registry and BioBank lists: Southeast Tissue Alliance, Inc. - SETA lists: National Biobank of Finland lists: CDC Cell and DNA Repository lists: ILSbio lists: California Cryobank, Inc. lists: ETEX Corporation lists: Leiomyosarcoma Cell and DNA Repository lists: HIV Biobank lists: Human Reference Genetic Material Repository lists: Hema-Quebec lists: LifeSource lists: National Temporal Bone Pathology Resource Registry lists: Blood Borne Pathogens Laboratory lists: Susan G. Komen Tissue Bank lists: Ohio State Biorepository lists: Alabama Organ Center lists: TRACK TBI Network lists: National Stem Cell Bank lists: Bioreclamation lists: Biobanque de Picardie lists: Ontario Tumour Bank lists: UK Stem Cell Bank lists: Fox Chase Biosample Repository Core Facility lists: Loma Linda University Cancer Center Biospecimen Laboratory lists: Barth Syndrome Biorepository lists: Interpore Cross International lists: Human Tissue Resource Network lists: California Transplant Services lists: National Cancer Institute Biorepositories lists: LifeCenter Organ Donor Network lists: HemaCare Corp. lists: Human Brain and Spinal Fluid Resource Center lists: Brain and Body Donation Program lists: Kings College London Infectious Diseases BioBank lists: Conticabase - European Sarcoma Database and Tumour Bank lists: Upstate New York Transplant Services lists: Donor Services of Indiana lists: Minnesota Liver Tissue Cell Distribution System lists: Research Tissue Repository - University of Connecticut lists: Mount Sinai Biobank lists: Rocky Mountain Tissue Bank lists: LifeCenter Northwest lists: International Histocompatibility Cell and DNA Bank lists: Regional Tissue Bank lists: Northwest Tissue Services lists: Washington University Tissue Bank lists: Capital Biosciences lists: Lawson Brain Tumour Tissue Bank lists: Andalusian Regional Tumour Bank lists: Protein Biotechnologies lists: Brainbow mouse resource at Jackson Labs lists: RTI Donor Services lists: University Andrology Laboratory lists: Cancer Control using Population-based Registries and Biobanks lists: UCSD Experimental Neuropath Laboratory lists: BioRep lists: da Vinci European Biobank lists: Wisconsin Tissue Bank lists: Indiana Organ Procurement Organization - IOPO lists: Quebec Leukemia Cell Bank lists: LifeBanc lists: Alzheimer's and Dementia Resource Center lists: Tayside Tissue Bank lists: Biobank Suisse lists: Florida Brain Bank lists: Erasmus MC Tissue Bank lists: Hackensack University Tissue Bank lists: World BioBank lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Tumorbank Basel Foundation lists: LifeLink Foundation lists: Gift of Hope Organ and Tissue Donor Network lists: St. Gallen Lung Biopsy Biobank lists: UNOS - United Network for Organ Sharing lists: UCSF AIDS Specimen Bank lists: MD Anderson Pancreas Tissue Bank lists: Kentucky Organ Donor Affiliates (KODA) lists: German Biobank Registry lists: Tennessee Donor Services lists: UC Davis Biorepository lists: MD Anderson Gynecologic Cancer Tissue Bank lists: Alamo Tissue Service, Ltd. lists: NeuroBiobank Munich lists: Brain-Net lists: Duke University Kathleen Price Bryan Brain Bank lists: Fairfax Cryobank lists: Lifeline of Ohio lists: University of Pittsburgh Brain Tissue Donation Program lists: Medical University of Vienna Institute of Neurology lists: NMDS - New Mexico Donor Services lists: South Carolina Biorepository System lists: CryoLife, Inc. lists: Tissue Banks International - TBI lists: NDRI Dorsal Root Ganglia Program lists: University of Texas Tumor Bank lists: Zebrafish International Resource Center lists: RLS Foundation Brain Bank lists: Dementia Brain Bank Research Program lists: St. Louis University Alzheimer's Brain Bank lists: Beta Cell Biology Consortium lists: UMKC Neuroscience Brain Tissue Bank and Research Laboratory lists: Parkinsons UK Brain Bank Duplicate lists: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository lists: University of Rochester Program for Brain Tumors and Spinal Tumors lists: Case Western Reserve Tissue Procurement and Histology Core Facility lists: Human Tissue Resource Network lists: Boston University Biospecimen Archive Research Core lists: Adenoma Polyp Tissue Bank lists: Brown Brain Tissue Resource Center lists: Texas A and M Health Science Center MSC Distribution lists: JAX Cre Repository lists: Jackson Laboratory Neurobiology lists: WaNPRC Pathology and Tissue Program lists: Geisinger Biobank lists: KI Biobank lists: KI Biobank - KOL lists: Cell Line Knowledge Base lists: KI Biobank - SCI lists: Janus Serum Bank lists: KI Biobank - GEMS lists: KI Biobank - TBI lists: KI Biobank - EIMS lists: KI Biobank - IMSE lists: Vector Database lists: KI Biobank - BROAD lists: KI Biobank - SBP lists: KI Biobank STAGE-ADHD lists: KI Biobank - STANLEY lists: KI Biobank - STAR lists: KI Biobank - EuroClot lists: KI Biobank - Economical Behavior lists: CATSS - Child and Adolescent Twin Study in Sweden lists: DOGSS lists: UMAS University Hospital - Biobanks of the Department of Clinical Pathology and Cytology lists: KI Biobank - SATSA lists: FaceBase Biorepository lists: KI Biobank - SALTY lists: KI Biobank - STAGE lists: KI Biobank - TwinGene lists: BIOAIR - BIOmarkers in severe Chronic AIRway Disease lists: KI Biobank - NOAK lists: OLIN - Obstructive Lung disease in Northern Sweden lists: Cancer of the Prostate in Sweden (CAPS) lists: KI Biobank - CEFALO lists: ICAP - Integrated analysis of prostate cancer lists: LIBRO-1: Individualized prediction and prevention of breast cancer lists: KI Biobank - PROCAP lists: SCALE - Scandinavian lymphoma etiology lists: SPSAC - Stockholm PSA Cohort lists: KI Biobank - Tissue Biobank lists: KI Biobank - CEFAM lists: KI Biobank - PAROKRANK lists: KI Biobank - Sodertaljehjartan lists: CreZOO lists: European Mouse Mutant Archive lists: Toronto Centre for Phenogenomics lists: CMMR - Canadian Mouse Mutant Repository lists: NHMRC Australian PhenomeBank lists: Australian Phenomics Network lists: International Mouse Phenotyping Consortium (IMPC) lists: ZMP lists: Sanger Mouse Resources Portal lists: Chimpanzee Biomedical Research Resource lists: Owl Monkey Breeding and Research Resource lists: Squirrel Monkey Breeding and Research Resource lists: Human Developmental Biology Resource lists: MouseBook lists: Ambystoma Genetic Stock Center lists: Chordoma Foundation Biobank lists: Biobank Ireland Trust lists: UCSF Brain Tumor Tissue Bank lists: Bloomington Drosophila Stock Center lists: NIDDK Central Repository lists: VA Biorepository Brain Bank lists: University of Florida DNA and Tissue Bank lists: Wake Forest Cynomolgus Breeding Colony lists: CCUG: Culture Collection; University of Goteborg; Sweden lists: Dictyostelium discoideum genome database lists: Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center lists: NCI Breast and Colon Cancer Family Registries lists: British Columbia Breast Cancer Tumour Bank lists: Wake Forest Vervet Research Colony lists: NIMH Stem Cell Center lists: Musculoskeletal Transplant Foundation - MTF lists: NIMH Repository and Genomics Resources lists: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C lists: Collaborative Studies on Genetics of Alcoholism lists: National Swine Resource and Research Center lists: National Center for Research Resources - Primate Resources lists: Confederation of Cancer Banks lists: zfishbook lists: SIU CADRD Dementia Brain Autopsy Program lists: Allograft Resources lists: AASK Clinical Trial and Cohort Study lists: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France lists: Stanford Center for Narcolepsy lists: Xenopus Gene Collection lists: Mammalian Gene Collection lists: Parkinsons UK Brain Bank lists: Zebrafish Gene Collection lists: Stanley Brain Collection lists: Boston Area Community Health Survey lists: Central New York Eye and Tissue Bank lists: Chromosome 7 Annotation Project lists: New York Brain Bank at Columbia University lists: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource lists: National Cell Repository for Alzheimer's Disease lists: NIA Aged Rodent Colonies lists: Knockout Mouse Project Repository lists: NINDS/UCLA Repository for Parkinson's Disease Mouse Models lists: Aging Cell Repository lists: Mouse Mutagenesis Center for Developmental Defects lists: National NeuroAIDS Tissue Consortium lists: NIA Nonhuman Primate Tissue Bank lists: National Alzheimer's Coordinating Center lists: NIA Mutant Mouse Aging Colony Handbook lists: JAX Mice: Neural Tube Defects lists: Caenorhabditis Genetics Center lists: Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core lists: NUgene Project lists: JAX Neuroscience Mutagenesis Facility lists: Hyper Cell Line Database lists: CHARTER - CNS HIV Antiretroviral Therapy Effects Research lists: BayGenomics lists: Alzheimer's Disease Cooperative Study lists: Baboon Research Resouces lists: Rhesus Monkey Breeding and Research lists: Mouse Mutant Resource lists: EMD4Biosciences lists: German Gene Trap Consortium lists: STRIDE Virtual Biospecimen Bank lists: Stanford/VA Aging Clinical Research Center lists: Spanish National Tumour Bank Network lists: Bioserve Global BioRepository lists: Saint-Luc Tumour Bank lists: Virgin Health Bank lists: UM Brain Endowment Bank lists: Manitoba Breast Tumor Bank lists: NIMH Brain Tissue Collection lists: UCL-RFH BioBank lists: Coriell Institute Stem Cell Biobank lists: MassGeneral Institute for Neurodegenerative Disease lists: Mayo Clinic Jacksonville: Neuropathology and Microscopy lists: NYU Alzheimer's Disease Center lists: Brain Research Institute Biobank Resources lists: Johns Hopkins Alzheimer's Disease Research Center lists: Rush Alzheimer's Disease Center lists: Massachusetts Alzheimer's Disease Research Center lists: University of Kentucky's Alzheimer's Disease Center lists: Michigan Alzheimer's Disease Center Brain Bank lists: Washington University Knight Alzheimer's Disease Research Center lists: Mount Sinai Alzheimer's Disease Research Center lists: Taub Institute for Research on Alzheimers Disease and the Aging Brain lists: Institute for Basic Research in Developmental Disabilities lists: Vietnam Era Twin Registry Biospecimen Repository lists: Study of Womens Health Across the Nation (SWAN) Repository lists: Dynamics of Health Aging and Body Composition (Health ABC) lists: University of Pennslyvania Brain Bank lists: Layton Center Biomarkers and Genetics lists: MUSC Center on Aging Campbell Neuropathology Laboratory lists: UT Southwestern ADC Brain Tissue Donation Program lists: KI Biobank - Parkinson lists: KI Biobank - EXT lists: GIA Brain Bank Program lists: KI Biobank - ALF lists: KI Biobank - HARMONY lists: Twin Study of Child and Adolescent Development - TCHAD lists: SHEEP - Stockholm Heart Epidemiology Program lists: CreZoo lists: Fleming Database lists: Los Angeles Family and Neighborhood Survey lists: Health and Retirement Study lists: Iowa 65+ Rural Health Study lists: National Long Term Care Survey lists: National Social Life Health and Aging Project (NSHAP) lists: Framingham Heart Study lists: Integrated Cell Lines lists: Chronic Renal Insufficiency Cohort Study lists: PrecisionMed lists: Biopta lists: Manhattan HIV Brain Bank lists: LifeGene lists: Puget Sound Blood Center lists: Fisher BioServices lists: National Psoriasis BioBank lists: StemCure Tissue Banking lists: ProMedDx lists: Biological Resource Centre - National Institute for Cancer Research lists: Coriell Biobank lists: StemSave lists: Dublin Brain Bank lists: Mayo Mitochondrial Disease Biobank lists: NIA Aged Rodent Tissue Bank lists: MVZ Collections lists: CARTaGENE lists: European Collection of Cell Cultures lists: UK DNA Banking Network lists: Biobanc USA lists: Rutgers Cell and DNA Repository lists: Genetic Alliance Biobank lists: Hunt Biobank lists: Advanced Biohealing, Inc. lists: Edinburgh Brain and Tissue Banks lists: JCM lists: Movement Disorders Biobank lists: Surgical Biologics - a MiMedx Group Company lists: Chernobyl Tissue Bank lists: Tissue Solutions lists: Conversant Biologics Inc. lists: Narayana Hrudayalaya Tissue Bank and Stem Cell Research Center lists: AlloSource lists: PathServe lists: UC Davis Alzheimers Disease Center - Resources lists: Asterand lists: RTI Biologics lists: Mayo Clinic Biobank lists: Lifelines Biobank lists: Mayo Validation Support Services Biobank lists: LifeNet Health lists: Medical Biobank lists: Fraunhofer Institute for Biomedical Engineering lists: BWH Specimen Bank lists: University of Minnesota Bionet - Academic Health Center lists: DF/HCC DNA Resource Core lists: Indiana Alzheimer Disease Center lists: UK Biobank lists: National Institute on Drug Abuse Center for Genetic Studies lists: Oregon Brain Bank lists: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) lists: Northwestern CNADC Tissue Bank / Neuropathology Core lists: Loyola University Medical Center / Hines VA Brain Bank lists: Trinity Biobank lists: SAPALDIA lists: Ohio U Diabetes Endocrine Biorepository lists: National Cell Culture Center lists: Diabetic Complications Consortium lists: Xenbase lists: Blueprint Epigenome lists: EBiSC lists: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) lists: Parkinson's Progression Markers Initiative lists: OriGene lists: University of Nottingham NASC Nottingham Arabidopsis Stock Centre is related to: Rat Resource and Research Center is related to: Honey Bee Brain EST Project is related to: Islet Cell Resource Centers is related to: Special Mouse Strains Resource is related to: NIH Human Pluripotent Stem Cell Registry is related to: Harvard Brain Tissue Resource Center is related to: Louisiana Organ Procurement Agency - LOPA is related to: Washington Regional Transplant Community - WRTC is related to: Minnesota Liver Tissue Cell Distribution System is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: National Swine Resource and Research Center is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: Mouse Mutagenesis Center for Developmental Defects is related to: NIA Mutant Mouse Aging Colony Handbook is related to: Manhattan HIV Brain Bank is related to: National Institute on Drug Abuse Center for Genetic Studies is related to: International Mouse Strain Resource is related to: Jackson Laboratory is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: GenitoUrinary Development Molecular Anatomy Project is related to: Coriell Cell Repositories is related to: NICHD Brain and Tissue Bank for Developmental Disorders is related to: Human Brain and Spinal Fluid Resource Center is related to: UM Brain Endowment Bank has parent organization: One Mind for Research has parent organization: Neuroscience Information Framework |
The community can contribute to this resource, Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_143622 | https://neuinfo.org/mynif/search.php?q=*&cf=Biospecimen&t=indexable&nif=nlx_143622-1 http://neuinfo.org/onemind/index.php?q=*&b=0&r=20 | SCR_004193 | One Mind: One Voice Bio-repository Cosmic Landscape, One Mind Biospecimen Banks | 2026-07-27 09:31:57 | 0 | ||||||
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UD Chick EST Project Resource Report Resource Website 10+ mentions |
UD Chick EST Project (RRID:SCR_002236) | cell repository, biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created. | gene, avian, cdna, chicken, clone, cytokine, dna, homology, immunology, mammalian, molecular, nucleotide, poultry, receptor, sequence, splenocyte, t cell |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Delaware; Delaware; USA |
PMID:16554550 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20971 | SCR_002236 | U.D. Chick EST Database, University of Delaware Chick EST Project, University of Delaware Chick EST Database | 2026-07-27 09:31:25 | 18 | |||||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, service resource, data analysis service, production service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-07-27 09:32:22 | 36 | |||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | analysis service resource, service resource, data analysis service, production service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-07-27 09:32:44 | 0 | |||
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UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-07-27 09:32:43 | 0 | |||||||||
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Chicken Gene Nomenclature Consortium Resource Report Resource Website 1+ mentions |
Chicken Gene Nomenclature Consortium (RRID:SCR_004966) | CGNC | service resource, narrative resource, data or information resource, data repository, database, standard specification, international standard specification, storage service resource | International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups. | orthology, ortholog, human, gene, nomenclature, prediction | has parent organization: Mississippi State University; Mississippi; USA | PMID:19607656 | Account required, The community can contribute to this resource | nlx_93177 | http://www.agnc.msstate.edu/Default.aspx | SCR_004966 | 2026-07-28 09:41:11 | 1 |
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