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The Mouse Genome Database genotypes::phenotypes.

Nucleic acids research | Jan 16, 2009

The Mouse Genome Database (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. Information in MGD is obtained from diverse sources, including the scientific literature and external databases, such as EntrezGene, UniProt and GenBank. In addition to its extensive collection of phenotypic allele information for mouse genes that is curated from the published biomedical literature and researcher submission, MGI includes a comprehensive representation of mouse genes including sequence, functional (GO) and comparative information. MGD provides a data mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. MGI can be accessed by a variety of methods including web-based search forms, a genome sequence browser and downloadable database reports. Programmatic access is available using web services. Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.

Pubmed ID: 18981050 RIS Download

Mesh terms: Alleles | Animals | Databases, Genetic | Genes | Genome | Genomics | Genotype | Internet | Mice | Phenotype | Software

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This is a list of tools and resources that we have found mentioned in this publication.


ZFIN

ZFIN is a Model Organism Database that serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. ZFIN includes (i) access to images with associated curated data, (ii) gene expression and phenotype data, (iii) zebrafish models of human diseases, (iv) genomic features and molecular details, (v) a genome browser, (vi) transcripts, (vii) antibodies and (viii) a community wiki for protocols and antibodies. ZFIN welcomes direct data submissions. If you would like to make your unpublished expression or phenotype data available to the community, you can submit this data to ZFIN using Phenote program or contact zfinadmn@zfin.org for additional options and support. Additionally, data is downloadable as text files and available in the data mining platform zebrafishmine (zebrafishmine.org).

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HGNC

A worldwide authority that approves standardized nomenclature to gene name and symbol (short-form abbreviation) for each known human gene and stores all approved symbols in the HGNC database. Approved symbols are also browse-able by chromosome. Each symbol is unique and each gene is only given one approved gene symbol. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse. Over 38,000 symbols have been approved; the vast majority of these are for protein-coding genes, but also include symbols for pseudogenes, non-coding RNAs, phenotypes and genomic features. Individual new symbols are requested by scientists, journals and databases, and groups of new symbols by those working on gene families or specific regions of the genome. Gene symbol and name proposals may be submitted to them to be accredited with HGNC approved nomenclature for use in publications, databases and presentations.

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RGD

Centralized database that collects, manages, and distributes data generated from ongoing rat genetic and genomic research efforts and makes these data widely available to the scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. It also facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include a comprehensive description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

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