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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Cytokine Family Database Resource Report Resource Website 1+ mentions |
Cytokine Family Database (RRID:SCR_008134) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases. | family, fish, gene, amphibian, bird, cdna, chemokine, cow, cytokine, genome, human, mammalian, mouse, oncogene, phylogenetic, protein, rat, receptor, reptile, virus |
is listed by: 3DVC has parent organization: Kumamoto University; Kumamoto; Japan |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20948 | http://cytokine.medic.kumamoto-u.ac.jp/ | SCR_008134 | SciCrunch Registry | dbCFC | 2026-10-17 01:33:25 | 1 | ||||||
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Tetraodon Genome Browser Resource Report Resource Website 1+ mentions |
Tetraodon Genome Browser (RRID:SCR_007079) | data or information resource, database, portal, topical portal | The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute. | duplication, element, euchromatic, evolution, exon, fish, gene, genetic, actinopterygians, aganth, ancestor, cartilaginous, cdna, chromosome, coding, collagen, cytokine, diversity, genome, genomic, heritage, hormone, human, interchromossomal, intergenic, intron, karyotype, lineage, mammal, molecule, mouse, nigroviridis, protein, proteome, pufferfish, receptor, region, selenoprotein, sequence, size, specie, synteny, system, takifugu, tetraodon, transposable, vertebrate | nif-0000-20997 | SCR_007079 | SciCrunch Registry | TGB | 2026-10-17 01:26:51 | 8 | ||||||||||
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HGNC Resource Report Resource Website 1000+ mentions |
HGNC (RRID:SCR_002827) | controlled vocabulary, data or information resource, database | Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs. | gene, owl, gene symbol, phenotype, nomenclature, gene family, gene groups, genomic, proteomic, ortholog, web service, locus, protein coding, genetics, gold standard, bio.tools, FASEB list, GCBR, ELIXIR Core Data Resource, DRKB |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: INFEVERS is related to: VGNC has parent organization: University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom |
NHGRI U24HG003345 | PMID:36243972 PMID:32747822 PMID:34615987 PMID:33152070 |
Free, Freely available | biotools:genenames.org, nif-0000-02955, r3d100010901 | http://bioportal.bioontology.org/ontologies/HUGO, https://bio.tools/genenames.org, https://doi.org/10.17616/R3XC80 | SCR_002827 | SciCrunch Registry | HUGO symbols, HGNC Database, HGNC - HUGO Gene Nomenclature Committee, HUGO Gene Nomenclature Committee, Human Genome Organization Gene Symbols | 2026-10-17 01:25:36 | 1134 | |||||
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3DVC Resource Report Resource Website |
3DVC (RRID:SCR_001377) | 3DVC | community building portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content. | cell, model, biological structure, molecule |
lists: Albinism database lists: ButterflyBase lists: G2P Knowledge Centre lists: Bio-Job.org lists: RettBASE: IRSF MECP2 Variation Database lists: Resource for Biocomputing Visualization and Informatics lists: National Center for Integrative Biomedical Informatics lists: Genome Network Platform lists: NeuroExplorer lists: Open Provenance Model lists: BarleyBase lists: BioModels lists: Arabidopsis Reactome lists: MEDLINE lists: bioDBcore lists: GermOnline lists: GlycoMapsDB lists: SNPHunter lists: Allen Institute for Brain Science Sleep Study lists: Coddle-Codons Optimized to Discover Deleterious LEsions lists: MicroArray and Gene Expression Markup Language lists: Fungal Genome Initiative lists: EMDataResource.org lists: University of Southern California LONI Software lists: Ontology Development and Information Extraction lists: Software Distribution Sets lists: L-Measure lists: UCSF Chimera lists: Zebrafish Neurophenome Project Database lists: Standards-based Infrastructure with Distributed Resources lists: HapMap 3 and ENCODE 3 lists: NCBI BioProject lists: SEQanswers Wiki lists: NIF Data Federation lists: SMD lists: SoyBase lists: modelcrop.org lists: BiGG Database lists: FSST - Functional Similarity Search Tool lists: LHP LHDL lists: Open Provenance Model Vocabulary lists: DiseaseMeth lists: neuroVIISAS lists: Predictive Networks lists: SitEx lists: NRCAM lists: DisGeNET lists: MCMBB lists: BARD lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: Comparative Toxicogenomics Database (CTD) lists: PomBase lists: Stanford University HIV Drug Resistance Database lists: Database of Chemical Compounds and Reactions in Biological Pathways lists: UCSD-Nature Signaling Gateway Molecule Pages lists: IntAct lists: The WWW Virtual Library: Model Organisms lists: Helicobacter Pylori Database of Protein Interactomes lists: Genes to Cognition: Neuroscience Research Programme lists: neuroConstruct lists: ModelDB lists: 3DViewnix lists: TMRPres2D lists: Ikaros Project lists: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING lists: Interagency Modeling and Analysis Group lists: Annozilla (Annotea on Mozilla) lists: Artificial Selected Proteins/Peptides Database lists: Cancer Chromosomes lists: CATMA - Complete Arabidopsis Transcriptome MicroArray lists: Combinatorial Extension (CE) lists: ChemDB: The UC Irvine ChemDB lists: CluSTr lists: CTDatabase lists: DRC - Database of Ribosomal Crosslinks lists: Gene Expression in Tooth Database lists: GenoBase lists: GPX-Macrophage lists: Hetero-compound Information Centre- Uppsala lists: IMG lists: InSatDb lists: InterDom lists: IPD-HPA - Human Platelet Antigens lists: Max Planck Unified Proteome Database lists: Molecular Modelling DataBase lists: MegaMotifbase lists: Metalloprotein Site Database lists: MitoDat - Mendelian Inheritance and the Mitochondrion lists: Madison Metabolomics Consortium Database lists: Olfactory Receptor DataBase lists: SUPERFAMILY lists: EyeBrowse lists: Allen Institute Mouse Diversity Study lists: BIRD - Bio Info R and D lists: Bioinformatics Links Directory lists: Electroencephalogram Database: Prediction of Epileptic Seizures lists: Human Protein-Protein Interaction Mining Tool lists: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki lists: Systems Biology Workbench lists: CellML lists: MathML lists: AraCyc lists: Biochemical Pathways database lists: CellML Model Repository lists: Cytokine Family Database lists: Bacterial Genomes lists: U.S. Pig Genome Project lists: ComBase: A Combined Database For Predictive Microbiology lists: GeneWindow lists: Comprehensive Systems-Biology Database lists: Candidate Genes to Inherited Diseases lists: MeGX lists: Mammalian Phosphorylation Resource lists: Efficient Mixed-Model Association lists: Proteome Analyst PA-GOSUB lists: PubCrawler lists: Conical: The Computational Neuroscience Class Library lists: Gene Expression Profile Analysis Suite lists: Adaptive Poisson-Boltzmann Solver lists: Aggrescan: The Hot Spot Finder lists: Distributed Annotation System lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: DNAWorks at Helix Systems lists: Microarray DB lists: Gene Relationships Across Implicated Loci lists: SEQtools lists: DeRisi Lab lists: Protein Subcellular Location Image Database lists: Open Information Integration lists: Metagenomics Program at JGI lists: BrainPeps lists: EGAN: Exploratory Gene Association Networks lists: CBioC lists: OrChem lists: Generic GO Term Finder lists: G-node portal electrophysiology data sharing lists: LegumeIP lists: Roadmap Epigenomics Project lists: TrakEM2 lists: ATID: Alternative Translational Initiation Database lists: linked life data - a semantic data integration platform for the biomedical domain lists: Crux tandem mass spectrometry analysis software lists: CellProfiler Analyst lists: Scirus - for scientific information only lists: SRS lists: KEGG lists: Antibodypedia lists: SWISS-MODEL Repository lists: BTKbase lists: ExTopoDB lists: MINAS - Metal Ions in Nucleic AcidS lists: Tripod lists: NIH electronic Research Materials catalogue lists: Alliance for Cellular Signaling Molecule Pages Database lists: Death Domain database lists: Cube-DB lists: OntoQuest lists: EASE: the Expression Analysis Systematic Explorer lists: Greglist lists: Chloroplast Genome Database lists: Montage RTS2000 lists: BGI-RISe - Beijing Genomics Institute Rice Information System lists: ApiDB CryptoDB lists: Chilibot: Gene and Protein relationships from MEDLINE lists: AutDB lists: DAVID lists: Dataverse Network Project lists: Binding MOAD lists: Biological Magnetic Resonance Data Bank (BMRB) lists: RNAhybrid lists: RegulonDB lists: Artemis: Genome Browser and Annotation Tool lists: Genomedata lists: CATSS - Child and Adolescent Twin Study in Sweden lists: Viking Viewer for Connectomics lists: SpliceDB lists: Galaxy lists: SPM lists: Hyper Cell Line Database lists: MeGX has parent organization: University of California at San Diego; California; USA |
NSF 1216893 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152536 | http://www.3dvcell.org/conference-toward-3d-virtual-cell | SCR_001377 | SciCrunch Registry | 3D Virtual Cell | 2026-10-17 01:24:54 | 0 | |||||
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University of California at San Francisco; California; USA Resource Report Resource Website 10+ mentions |
University of California at San Francisco; California; USA (RRID:SCR_010605) | UCSF | university | Public research university in San Francisco, California. Part of University of California system. Dedicated entirely to health sciences. Major center of medical and biological research and teaching. Ranked as one of top universities in biomedical field in USA and around world. | institution, university, health science, medical, biological, teaching, center, biomedical |
is affiliated with: Diabetes Research Centers is related to: NCIRE is related to: ONE Study is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Diabetic Foot Consortium has parent organization: University of California; California; USA is parent organization of: DOCK is parent organization of: MochiView is parent organization of: Kravitz Dataset 2 is parent organization of: uManager is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: CryptoBase is parent organization of: Resource for Biocomputing Visualization and Informatics is parent organization of: Hyperpolarized MRI Technology Resource Center is parent organization of: Sherlock is parent organization of: Center for Imaging of Neurodegenerative Diseases is parent organization of: WikiPathways is parent organization of: International Gene Trap Consortium is parent organization of: Microstructural correlation toolbox is parent organization of: NUTMEG is parent organization of: AltAnalyze - Alternative Splicing Analysis Tool is parent organization of: Integrative Modeling Platform is parent organization of: UCSF Spot is parent organization of: Allelic Variations of The XP Genes is parent organization of: Edinburgh Postnatal Depression Scale is parent organization of: AIDS and Cancer Specimen Resource is parent organization of: UCSF DNA Bank is parent organization of: Babel is parent organization of: UCSF DataShare is parent organization of: Scientific Data Sharing Project is parent organization of: ModBase is parent organization of: UCSF Laboratory for Visual Neuroscience is parent organization of: UCSF AIDS Specimen Bank is parent organization of: Gene Map Annotator and Pathway Profiler is parent organization of: ExPANdS is parent organization of: UCSF Center for AIDS Prevention Studies (CAPS) is parent organization of: HOLLOW is parent organization of: MAPPFinder is parent organization of: iBioSeminars is parent organization of: Bioelectromagnetism Matlab Toolbox is parent organization of: UCSF Brain Tumor Tissue Bank is parent organization of: Krogan Lab Interactome Database is parent organization of: BayGenomics is parent organization of: CanPredict is parent organization of: MODELLER is parent organization of: DeRisi Lab is parent organization of: CTSpedia is parent organization of: Kravitz Dataset1 is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center is parent organization of: Clinical Research Resource HUB is parent organization of: National Bio-Organic Biomedical Mass Spectrometry Resource Center is parent organization of: Program to Reduce Incontinence by Diet and Exercise is parent organization of: Brain Health Registry is parent organization of: The Li Lab at UCSF is parent organization of: UCSF Nikon Imaging Center is parent organization of: UCSF School of Medicine; California; USA is parent organization of: Microarrays.org is parent organization of: University of California, San Francisco School of Pharmacy is parent organization of: PRICE is parent organization of: HMMSplicer is parent organization of: ArrayOligoSelector is parent organization of: stepNorm is parent organization of: National Center for X-ray Tomography is parent organization of: SURPI is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging is parent organization of: PSCBS is parent organization of: Sparky is parent organization of: Cytokine Registry is parent organization of: Protein Prospector is parent organization of: University of California San Francisco Diabetes Research Center Mouse Genetics Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Islet Production Core Facility is parent organization of: University of California San Francisco Parnassus Flow Cytometry Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility is parent organization of: University of California San Francisco Diabetes Research Center Microscopy Core Facility is parent organization of: University of California San Francisco Diabetes Research Center is parent organization of: University of California San Francisco Diabetes Research Center Mouse Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Mouse Metabolism and Imaging Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Human Metabolism Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center Genetics and Genomics Core is parent organization of: University of California San Francisco Nutrition and Obesity Research Center is parent organization of: Cystic Fibrosis Center - University of California San Francisco is parent organization of: UCSF ChimeraX is parent organization of: MotionCor2 is parent organization of: Clonotator is parent organization of: FoXS is parent organization of: covidcounties.org is parent organization of: DoubletFinder is parent organization of: syndRomics is parent organization of: PhotometryBox is parent organization of: University of California at San Francisco Immunology Lab Core Facility is parent organization of: Similarity Ensemble Approach is parent organization of: University of California at San Francisco Advanced Microscopy Core Facility is parent organization of: University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility is parent organization of: UCSF Helen Diller Family Comprehensive Cancer Center Flow and Cell Sorting Core Facility |
nlx_57854, GRID grid.266102.1; ISNI 0000 0001 2297 6811; Crossref Funder ID 100008069; Wikidata Q1061104 | https://ror.org/043mz5j54 | SCR_010605 | SciCrunch Registry | UC San Francisco, The University of California, San Francisco, University of California San Francisco, University of California at San Francisco | 2026-10-17 01:27:39 | 13 | |||||||
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Kumamoto University; Kumamoto; Japan Resource Report Resource Website |
Kumamoto University; Kumamoto; Japan (RRID:SCR_004102) | institution, university |
is related to: Center for Animal Resources and Development is parent organization of: Cytokine Family Database |
SCR_004102 | SciCrunch Registry | 2026-10-17 01:34:54 | 0 |
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