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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Sep 3, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
tranSMARTResource, software resourcetranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal.source code, genetic, phenotype, gene, data storage repository, data analysis serviceSCR_005586(tranSMART, RRID:SCR_005586)used by: eTRIKS, RanchoBiosciencesLast checked downnlx_146211
Bio Resource for Array Genes DatabaseResource, data or information resource, databaseBio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissueSCR_000748(Bio Resource for Array Genes Database, RRID:SCR_000748)University of Arizona; Arizona; USA Last checked downnif-0000-10165
TRIMHAPResource, software resource, software applicationSoftware application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)gene, genetic, genomic, fortran, unixSCR_013512(TRIMHAP, RRID:SCR_013512)listed by: Genetic Analysis SoftwareLast checked downnlx_154683
NIA Mouse cDNA Project Home PageResource, database, biomaterial supply resource, data set, portal, material resource, data or information resourceProject portal housing NIA Mouse EST Project, NIA Mouse cDNA Clone Sets, a NIA Mouse Gene Index, NIA Mouse cDNA Database, and NIA Mouse Microarrays. Characteristics of NIA 15K Mouse cDNA Clone Set * ~15,000 unique cDNA clones were rearrayed among 52,374 ESTs from pre- and periimplantation embryos, E12.5 female gonad/mesonephros, and newborn ovary. * Up to 50% are derived from novel genes. * ~1.5 kb average insert size. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H3001A01 to H3159G07. * Handling of NIA 15k cDNA Clone Set(June3, 2000) Characteristics of NIA mouse 7.4K cDNA Clone Set * ~7407 cDNA clones with no redundancy within the set or with NIA Mouse 15K. * ~1.5 kb average insert size for short insert clones and ~2.5-3.0 kb average insert size for long-insert enriched clones.. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H4001A01 to H4079G07. * Handling of NIA mouse 7.4k cDNA Clone Set (similar to handling of NIA mouse 15K, to be updated) Individual Clones are available from ATCC and MRC geneservice, UK. To obtain Clone, search the database using either the rearrayed clone name or GenBank accession number at the Key Word Search page. Follow the link to the sequence information page for the rearrayed clone to obtain source clone ATCC number. Clicking the ATCC number will bring up the ATCC ordering page for the source clone. There is essentially no overlap between the two clone sets (7.4K and 15K) said Minoru S.H. Ko, M.D., Ph.D., head of the Developmental Genomics and Aging Section in the NIA's Laboratory of Genetics. In addition, all cDNA clones in the NIA 7.4K set were purified by single colony isolation and sequence-verified, and more than half were prepared by a new procedure that yields long full-length cDNAs (average size 3-4 kb). The NIA Mouse 15k and 7.4k Clone Set Data and Published Microarray Data are available for download. NIA Mouse Microarrays *Microarray Data Download * 60-mer Oligo Array Platform ** (A) NIA 22k Oligo Microarray Gene List (21939 gene features) ( Carter et al 2003 ) ** (B) Agilent Mouse Development Oligo Microarray Gene List ** ( Subset of Microarray (A): 20,280 gene features ) * Data Analysis Toolsembryonic, expression, fetal, gene, cdna, cell, clone set, human disease, microarray, mouse, mouse model, newborn, stem cell, tissue, cloneSCR_001472(NIA Mouse cDNA Project Home Page, RRID:SCR_001472)Intramural Research Program AgingNIAuses: ATCC, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-09471
The Biomedical Research Foundation - Current ResearchResource, topical portal, portal, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy.drug, electron microscopy, - flow cytometry, gene, abuse, alcohol, automated cell imaging, cancer, cloning, confocal and digital microscopy, dna, dna gene chip analysis, immunology, inflammation, ischemic disorder, liquid chromatography, magnetic resonance spectroscopy, mass spectrometry, monoclonal antibody production, neuroscience, oligonucleotide, peptide, polymerase chain reaction (pcr), positron emission tomography, sequencing, signal transduction, synthesis, tissue cultureSCR_001564(The Biomedical Research Foundation - Current Research, RRID:SCR_001564)Last checked downnif-0000-10446
BMAPBUILDERResource, software resource, software applicationSoftware application (entry from Genetic Analysis Software)gene, genetic, genomic, java, ms-windows, macos, unix, linuxSCR_007264(BMAPBUILDER, RRID:SCR_007264)listed by: Genetic Analysis SoftwareLast checked downnlx_154084
Honey Bee Genome ProjectResource, topical portal, portal, data or information resourceThe HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.gene, agricultural, allergy, antibiotic, apis mellifera, array, behavioral, biologist, chromosome, development, disease, genome, heath, honey bee, human, immunity, insect, mental heath, organism, pollination, reaction, resistance, sequence, traitSCR_002890(Honey Bee Genome Project, RRID:SCR_002890)Baylor University; Texas; USA Last checked downnif-0000-25604
C. elegans Gene Knockout ConsortiumResource, organism supplier, production service resource, biomaterial supply resource, material service resource, service resource, material resource, biomaterial manufactureTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The mission of the C. elegans Gene Knockout Consortium is to facilitate genetic research of this important model system through the production of deletion alleles at specified gene targets. We choose targets based on investigator requests. Strains produced by the consortium are freely available with no restrictions to any investigator. At one time, our capacity dictated that we restrict requests to five per lab. This restriction no longer holds. Investigators are encouraged especially to register requests for functionally related groups of genes. Consortium strains are distributed by the C. elegans Genetic Center (CGC). In most cases, when you use the Consortium web site to request an existing allele, your request is forwarded automatically to the CGC. However, if you indicate that an existing allele is not satisfactory for your research, (for whatever reason), you may request that we generate another allele for the same target. Any information generated by the Consortium is entered into the official C. elegans data repository, WormBase.gene, locus, knockout, genetic, research, model, allele, target, strain, deletion allele, gene targetSCR_003000(C. elegans Gene Knockout Consortium, RRID:SCR_003000)Oklahoma Medical Research Foundation related to: Caenorhabditis Genetics Center, WormBaseLast checked downnif-0000-30230
FlexGenOrganization, material resource, commercial organization, instrument supplierA biotechnology company that has developed technology for synthesizing custom microarrays, the FlexArrayer. Its is a desk-top sized instrument which allows the researcher to generate, in their own laboratory, either a custom oligonucleotide array in a single day or oligonucleotide pool in a few days. Recent developments in synthesis chemistry allows many modifications to be incorporated or for alternative chemistries to be considered.biotechnology, microarray, custom oligonucleotide array, oligonucleotide pool, oligonucleotide, gene, probe synthesis, target enrichment, probe design, biomolecule, dna sequencing, oligonucleotide synthesis, re-sequencingSCR_003902(FlexGen, RRID:SCR_003902)related to: READNALast checked downnlx_158237
TDTASPResource, software resource, software applicationSoftware application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)gene, genetic, genomic, fortran95, unix, ms-windowsSCR_004943(TDTASP, RRID:SCR_004943)listed by: Genetic Analysis SoftwareLast checked downnlx_154675
NIH Knockout Mouse Project (KOMP)Resource, topical portal, portal, data or information resourceA trans-NIH initiative to generate a comprehensive and public resource comprised of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. By capitalizing on efficiencies of scale and a centralized production effort, the project intends to make this catalog of mutants available in mouse strain C57BL/6 for two reasons: it is the most widely used strain and it is the strain for which complete genome sequence has been made available. The NIH KOMP initiative aims to: 1) use gene targeting to make the resource of null alleles, marked with a high utility reporter, preferably in C57BL/6; 2) support a repository to house the products of this resource as well as an additional "repatriation" effort to bring into repositories 1000 of the existing high priority mouse knockouts not already stored in a public repository; 3) develop improved C57BL/6 ES cells that show robust germline transmission, so that they may be used in a high throughput pipeline in generating this resource; and 4) implement a data coordination center which will make the status and relevant data of the production effort available to the research community. Towards those ends, NIH awarded five-year cooperative agreements totaling up to $47.2 million to two groups for the creation of the knockout mice lines. Recipients of those awards are Regeneron Pharmaceuticals, Inc., in Tarrytown, N.Y., and a collaborative team from Children's Hospital Oakland Research Institute (CHORI) in Oakland, Calif., the School of Veterinary Medicine, University of California, Davis (UC Davis); and the Wellcome Trust Sanger Institute in Hinxton, England. Under its cooperative agreement, the team plans to systematically create mouse ES cell lines in which 5,000 genes have been knocked out by gene targeting. The VelociGene division of Regeneron, will take aim at a different set of 3,500 genes. Both groups will utilize information from the finished mouse genome sequence to design targeting vectors, which will be built by large-scale, automated technologies. The combined collection of mouse ES cells with knockouts in 8,500 genes will be useful for producing knockout mice. In addition, The Jackson Laboratory will set up a Data Coordination Center that will allow the research community to track the scheduling and progress of knockout production. The center will also serve as a central information resource for all publicly available knockout mutants and will integrate with other databases that contain mouse DNA sequence, additional information on mouse genetics and information on the physical and biochemical characteristics of the knockout mice. The NIH has also provided $4.8 million to establish and support a repository for the Knockout Mouse Project. Finally, NIH awarded cooperative agreements to improve the efficiency of methods for creating knockout lines. They will focus on developing methods to create ES cell lines suitable for high-throughput gene targeting or trapping in C57BL/6.embryonic stem cell, c57bl/6, knock out mouse, gene, mutationSCR_005571(NIH Knockout Mouse Project (KOMP), RRID:SCR_005571)International Knockout Mouse Consortium , National Institutes of Health NIH, NIH Blueprint for Neuroscience Researchrelated to: Monarch Initiative, listed by: NIDDK Information Network, NIDDK Research ResourcesLast checked downnlx_145296
DBD - Slim Gene OntologyResource, software resource, software application, data or information resource, databaseDb for Dummies! is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree. The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from Platform: Windows compatiblegene ontology, gene, hierarchy, visualization, database or data warehouseSCR_005728(DBD - Slim Gene Ontology, RRID:SCR_005728)Db for Dummies! related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149185
GOtchaResource, analysis service resource, data analysis service, service resource, production service resourceGOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online toolfunction, protein, prediction, genome, annotation, gene, statistical analysisSCR_005790(GOtcha, RRID:SCR_005790)University of Dundee; Scotland; United Kingdom European Union fifth framework, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15550167Last checked downnlx_149269
Genotype-IBD Sharing Test Resource, software resource, software application, resourceSoftware package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, associationSCR_006257( Genotype-IBD Sharing Test , RRID:SCR_006257)Vanderbilt University; Tennessee; USA NHGRI, NIDDK, Vanderbilt Diabetes Centerlisted by: Genetic Analysis SoftwarePMID:14872409Last checked downnlx_154133
HDBaseResource, disease-related portal, data set, topical portal, portal, data or information resourceA community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse modelsdrug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathwaySCR_007132(HDBase, RRID:SCR_007132)Institute for Systems Biology; Washington; USA Huntington''s disease, ControlHereditary Disease Foundationuses: CytoscapeLast checked downnif-0000-00153
CardioGenomicsResource, topical portal, portal, data or information resourceThe primary goal of the CardioGenomics PGA is to begin to link genes to structure, function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease. This PGA will generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population. Such a data set will serve as a benchmark for future basic, clinical, and pharmacogenomic studies. Training and education are also a key focus of the CardioGenomics PGA. In addition to ongoing journal clubs and seminars, the PGA will be sponsoring symposia at major conferences, and developing workshops related to the areas of focus of this PGA. Information regarding upcoming events can be found in the Events section of this site, and information about training and education opportunities sponsored by CardioGenomics can be found on the Teaching and Education page. The CardioGenomics project came to a close in 2005. This server,, remains online in order to continue to distribute data that was generated by investigators under the auspices of the CardioGenomics Program for Genomic Applications (PGA). :Sponsors: This resource is supported by The National Heart, Lung and Blood Institute (NHLBI) of the NIH.genomics, clinical, genetic, environmental, stimulus, cardiovascular, disease, data, expression, gene, dna, polymorphism, population, pharmacogenomic, training, educationSCR_007248(CardioGenomics, RRID:SCR_007248)Harvard University; Cambridge; United States Last checked downnif-0000-30296
R/STEPWISEResource, software resource, software applicationSoftware application that is a stepwise approach to identifying recombination breakpoints in a sequence alignment (entry from Genetic Analysis Software)gene, genetic, genomic, rSCR_007420(R/STEPWISE, RRID:SCR_007420)listed by: Genetic Analysis SoftwareLast checked downnlx_154601, SCR_009103, nlx_154196
ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulationResource, data or information resource, data computation service, databaseA database is a of mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their co-expression and proteins known to be involved in miRNA processing. This database also contains three other navigation tools that can be used to find information relating to miRNA: 1.) Gene Annotations is an information retrieval system for miRNA target genes. It provides comprehensive information from sequence databases and allows to simultaneously search PubMed with all synonyms of a given gene. 2.) miRNA Motif Finder - Argonaute predicts miRNA motifs binding to the gene sequence of the user. The miRNA mature sequences are taken from Agronaute 2 database. miRNA Motif Finder - Custom predicts miRNA motifs binding to the gene sequence, both the gene sequence and miRNA mature sequences provided by the user. 3.) miRNA Statistics provides statistics for the mature miRNA sequences from Argonaute 2 as well as for the miRNA sequences uploaded by the user. It provides statitics on the individual nucleotide as well as pattern of nucleotides apperaing in the sequence.gene, metabolic and signaling pathways, mirna, protein-protein interaction, rna sequence databaseSCR_007553(ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation, RRID:SCR_007553)Heidelberg University; Baden-Wurttemberg; Germany Deutsche Forschungsgemein, Federal Ministry of Research and EducationLast checked downnif-0000-02567
CAGEResource, software resourceExpression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5''''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5''''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5''''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jpgene, gene expression, transcriptome, expression profiling, promoter identification, promoter, gene discovery, cdna, cdna library, genome annotation, genome, annotation, rna library, rna, mrnaSCR_007574(CAGE, RRID:SCR_007574)RIKEN related to: FANTOM DB, CAGE Basic Viewer for Mus musculusLast checked downnif-0000-02631
GASPResource, software resource, software applicationSoftware tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. (entry from Genetic Analysis Software)gene, genetic, genomic, fortran77, unix, dec-unix 4.0b, solaris 2.5, sgi-irix 6.2SCR_008703(GASP, RRID:SCR_008703)listed by: Genetic Analysis SoftwareLast checked downnlx_154313
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