Importantly, the institute is currently sequencing the genomes of 17 of the mostused strains of mouse in contemporary biology. Relational databases for biologists tutorial ismb02. Mgd represents mouse genetic, genomic and biological data of many kinds, including gene identification, allelic variants, sequence links, maps and mapping data, mutant and strain phenotype. Data records of mice with chronic fentanyl administration were added to mouse phenotype database. The mouse phenotype database consists of the raw data of behavioral tests from the mice strain that are published in articles.
Accepted october 1, 2009 abstract the mouse genome database mgd is a major. Generation of conditional mutations in every gene of the genome impc. Mouse phenome association database database containing results of genome wide association studies using publicly available data from the jax mouse phenome project. Mouse genome database mgd, gene expression database gxd, mouse models of human cancer database mmhcdb formerly mouse tumor biology mtb, gene ontology go.
The most efficient lims system to manage your mouse colony data. European conditional mouse mutagenesis program eucomm es cells 19. The mmr mouse variation database provides access to all genetic variants called from highthroughput exome and whole genome sequencing from mice exhibiting spontaneously arising mendelian disease phenotypes. The laboratory mouse is an invaluable model organism for investigating the genetic basis of human disease. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext.
The jax colony management system jcms was a free multiuser relational database system for managing research mouse colonies. Identify the or at least one genomic regions qtls that contribute to variation in the trait. To improve the previous version of mousenet genome biology 2008, a large volume of new microarray data derived from diverse biological contexts has been incorporated. Softmouse an online mouse colony management database and. The imsr is a searchable online database of mouse strains, stocks, and mutant es cell lines available worldwide, including inbred, mutant, and genetically engineered strains.
Work from the lab, your home or remotely with softmouse mouse colony management software online database and mouse breeding software in the cloud. Mgd is the highly curated, community model organism database for the laboratory mouse providing web and programmatic access to a complete catalog of mouse genes and genome features integrated with functional annotations, a comprehensive catalog of mutant alleles, phenotype. These data are integrated with the rest of data in mgi and exported to numerous other resources. Bult cj, krupke dm, begley da, richardson je, neuhauser sb, sundberg jp, eppig jt. Jul 11, 2015 a core part of the mouse genome informatics mgi resource is the collection of mouse mutations and the annotation phenotypes and diseases displayed by mice carrying these mutations. The recent availability of genomic sequence from several mouse inbred strains. However, identifying the specific phenotype causing dna sequence variations within a quantitative trait locus has been much more difficult. Support for jcms was provided by nigms, hhmi, and the jackson laboratory. Studies have demonstrated the efficacy of comparative mousehuman genomics to identify novel mechanisms of human disease progression, underscoring the need to make mouse strain data widely available for community access. Mouse genome data download wellcome sanger institute. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect. The mouse genome database mgd has been available to the scientific community via the web since 1994. This resource is a collaborative standardized collection of measured data on laboratory mouse strains and populations.
Gene set data for pathway analysis in mouse 4using the data the following examples use the knowledge base gene sets to run pathway analysis on a microarray gene expression data obtained from gene expression ominibusgse40261. Our growing catalogue of mammalian gene function is freely available for researchers. Breeding strategies for maintaining colonies of laboratory mice. Allele, phenotype and disease data at mouse genome. Mouse phenome database nucleic acids research oxford academic.
Mouse hapmap genetic maps for 94 inbred strains of mouse. January mtb has a publication in the 2015 database issue of nucleic acids research. These resources are tightly integrated and can be accessed as a single data resource, the mgi database. Additional terms or revisions may be requested through our issue tracker at github. Eucomm tools for functional annotation of the mouse genome ikmc. Nig mouse phenotype database is used to identify latent genetic components underlying quantitative complex traits based upon mouse intersubspecific genomic and phenotypic differences. Mouse genome informatics mgi is a free, online database and bioinformatics resource hosted by the jackson laboratory, with funding by the national human genome research institute nhgri, the national cancer institute nci, and the eunice kennedy shriver national institute of child health and human development nichd. The articles that report the behavior of the mouse strains that are maintained in the database are listed here. The jackson laboratory jax advocates adherence to the mouse strain nomenclature guidelines as described by the international committee on standardized genetic nomenclature for mice. Jcms is no longer being developed and is now unsupported. The mouse phenome database is a collaborative standardized collection of measured data on laboratory mouse strains and populations. Nov 21, 2012 mgd is the highly curated, community model organism database for the laboratory mouse providing web and programmatic access to a complete catalog of mouse genes and genome features integrated with functional annotations, a comprehensive catalog of mutant alleles, phenotype annotations, human disease model annotations, variation data and.
Mammalian phenotype mp browser browse for a human disease term to find mouse models. Mitdb is a subset of the portable dictionary of the mouse genome. The mp provides a standard underpinning to mouse phenotype descriptions for existing and future. Human phenotype ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. The annotations were generated by ucsc and collaborators worldwide. Available genotype resources and tools mouse snp data help data sets mouse gene marker search qtl archive projects include genotype data mpd search supports gene and marker. The mouse phenome database mpd has baseline phenotype data sets as well as studies of drug, diet, disease, and aging. Mouse phenome database nucleic acids research oxford. Mammalian phenotype ontology annotations query results summary. Existing software solutions for data management vary significantly in terms of cost.
Characterization of the phenotype of every mutated gene generation of models for human disease comparative analysis of disease relevant proteinmetabolic pathways. Mousemine is funded through a grant from the nihnhgri. Furthermore, the international mouse phenotyping consortium. The heart of any colony management program is an appropriate breeding scheme. Mgds goal is to advance understanding of human biology and disease by facilitating access to integrated genetics and genomic data for the laboratory mouse. From the collection of 20,029 protein coding genes all retrieved from the gencode database, we extracted the set of 2,472 onetoone human orthologs of these essential mouse genes eg, figure 1a, methods and the nonoverlapping set of 3,811 human orthologs of genes with known nonlethal phenotype nlg in homozygous mouse mutants.
Mouse phenome database mpd deltagen and lexicon knockout mice. Behavior analysis software mouse phenotype database. The jackson colony management system jcms is designed to meet a wide variety of colony management and phenotype data management needs for small to mediumsized laboratories. The mouse phenome database is a collaborative standardized collection of measured data on laboratory mouse. The use of mouse phenotype data to drive translational research into human disease has expanded rapidly with the. The mouse phenome project was launched a decade ago to complement mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public database, the mouse phenome database. Search for mutations or qtl based on phenotype, human disease, mutation type, gene, or genome location.
Integration of and access to knowledge about the laboratory mouse. The jax colony management system jcms is a free and supported multiuser relational database system for managing research mouse colonies. Data records of aldh3a2 knockout mice were added to mouse phenotype database. Hospital for sick children 1993 mouse genome database mgd at informatics. Mpd integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis.
Mouse genome database mgd, gene expression database gxd, mouse models of human cancer database mmhcdb formerly mouse. Welcome the softmouse team is honored to welcome former jax colony management system jcms, gmouse, mousehouseapp, mousehouse, filemaker pro and spreadsheet users who are looking for a same day supported, userfriendly rodent colony management system online software and database. The jackson laboratory utilizes a combination of breeding scheme and visible phenotype to genotype animals from its b6. Mar 26, 2008 several mouse database systems have been developed and published in the course of other large phenotype screening projects during the last years 1114, and a couple of additional mouse database systems are commercially available. Take advantage of the convenience of having your husbandry, sourcing, and efficacy evaluation needs met by jax. A database of mit microsatellite loci in the mouse. Details for chip packages such as this, the accnum mapping comes directly from the manufacturer. Our new tool set is built using r statistical software, python and d3. International mouse phenotyping consortium impc deciphering the mechanisms of developmental disorders dmdd contributed data sets. Disease connection search for a phenotype term to find relevant mutant genotypes. The jackson laboratory colony management system jcms is a software. Mouse genome informatics mgi is a free, online database and bioinformatics resource hosted by the jackson laboratory, with funding by the national human genome research institute. An inbred strain msmms was established from japanese wild mice, m.
A mutations genetic background may affect phenotype, including breeding. Inthisexperiment,microrna29bwasblockedbyantisenseoligonecleotides. Despite the existence of these highquality systems, we opted to develop a system for the needs of the gmc. Mouse genome data download the sanger institute made a major contribution to the reference genome sequence of the mouse. For general citation of mpd, this article may be used. Other mgi data resources include the gene expression database gxd, the mouse tumor biology database mtb, the gene ontology project go, mouse mine and the mousecyc database of biochemical pathways. Welcome to international microinjection tracking system.
The mouse phenome database has several datasets that can be searched by strain that may help. The mouse genome database mgd is the primary community knowledgebase for mouse phenotype and gene function and mouse models of human disease. It also includes protocols, projects, publications, and snp, variation, and gene expression studies. Th ese techniques have been developed and used by th e jackson laboratory for over 75 years. The goal of the imsr is to assist the international scientific community in locating and obtaining mouse resources for research. Eppig and the mouse genome database groupy the jackson laboratory, 600 main street, bar harbor, me 04609 usa received september 15, 2009. This directory contains a dump of the ucsc genome annotation database for the dec. Currently two databases present raw data for individual mouse strains. With unmatched depth it enables clinicians to record and analyse data with. Mouse strain phenotype database umlaut software, inc. The mouse genome database mgd is the community model organism knowledgebase for the laboratory mouse.
The jackson laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software or data will not. Mouse genome database mgd 2019 nucleic acids research. Tools for functional annotation of the mouse genome. Mouse hapmap genetic maps for 94 inbred strains of mouse and imputed genotypes using the niehsperlegen resequencing resource. Phenotype enrichment software tools transcription data analysis genomescale phenotypic data are available for many model organisms, yet existing tools to functionally interpret gene sets from these phenotypic data are largely based on mutagenesisderived phenotypes observed in mouse or human. Th ey are safe, reliable, economical, effi cient, and ensure that the mouse strains produced are genetically well defi ned. The jax patient derived xenograft pdx resource has information on over 400 pdx models.
Jan 21, 2007 the mapping of quantitative trait loci in rat and mouse has been extremely successful in identifying chromosomal regions associated with human diseaserelated phenotypes. Research tools and resources the jackson laboratory. Diversity outbred mice offer increased genetic heterozygosity, allelic diversity, and recombinatorial precision compared to traditional mouse mapping populations, making them. The mission of the mgd is to advance the use of the laboratory mouse as a model system for investigating. Open source project for behavior analysis software for movie protocol using imageep, see komada et al. Integrating mouse anatomy and pathology ontologies into a. The jackson laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software. Use this filemaker pro database with ourprimersdb below. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. The international mouse phenotyping consortium impc is a global effort to identify the function of every proteincoding gene in the mouse genome.
Gene ontology go mammalian phenotype mp human disease do alleles gene expression refsnp id genbankrefseq id uniprot id none contributing projects. The jackson laboratory, 600 main street, bar harbor, me 04609, usa. Jax mice bred and distributed from the jackson laboratory and charles river laboratories in europe and japan are bred using established practices that reduce. The jax synteny browser for mousehuman comparative. In addition, the following citation format may be used when mpd projects are referred to or mpd datasets used. Disease ontology do browser search or browse for a human phenotype term to find relevant human diseases with those phenotypes. Investigators name year project posted project title. Our data has such high resolution you can see vasculature in the liver, heart wall thickness, vilii in the bowel, the ventricles in the brain, the aorta, and much more. Recent improvements to mgd include integration of the latest mouse genome build grcm38, improved access to comparative and functional annotations for mouse genes and new uploads of phenotype data from the sanger institute mouse genetics program and the europhenome euph database. Please contact us with any other questions about the mammalian phenotype ontology this ontology is also used by the rat genome database. The jax synteny browser is organized as four main panels. Also includes protocols, projects and publications, and snp, variation and gene expression studies. Home impc international mouse phenotyping consortium. Founded in 1929, the jackson laboratory jax is an independent, nonprofit biomedical research institution with more than 2,200 employees who are passionate about our mission.
1452 150 523 243 149 1358 1245 29 895 1374 785 1453 95 529 173 762 1187 1281 392 312 1273 942 126 1312 921 1608 955 81 972 1250 109 220 1485 290 141 946