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June 10, 2019
GXD has developed an RNA-Seq and Microarray Experiment Search to quickly and reliably find specific mouse expression studies in ArrayExpress and GEO. Based on GXD's standardized metadata annotations, users can specify the age, anatomical structure, mutant alleles, strain and sex of samples of interest as well as experiment study type and key parameters. These searches, powered by controlled vocabularies and ontologies, can be combined with free text searching of experiment titles and descriptions. Search result summaries include linkouts to ArrayExpress and GEO, providing easy access to the expression data itself. Links to the PubMed entries for corresponding publications are also included.
GXD's annotation efforts focus on experiments that examine endogenous gene expression in wild-type and mutant mice. Studies from all developmental stages, including adult, are included. In addition, studies examining expression differences within and between species is available (although the metadata for the non-mouse samples is not). As is consistent with GXD's scope, studies using transgenic mice (i.e., animals containing randomly inserted transgenes); animals that have been manipulated, either by substances, surgical procedures, or diet regimens; cultured tissues; or cell lines are not included.
The RNA-Seq and microarray metadata index developed by GXD is comprised of all experiments currently available in ArrayExpress that fit the criteria described above. This includes thousands of experiments that were originally submitted to GEO. Prior to August 2016 ArrayExpress imported all experiments stored at GEO. Future work will incorporate the more recently submitted GEO experiments into the GXD RNA-Seq and Microarray Experiment index.
May 6, 2019
For the MGI 6.14 release:
  • We retired the MouseCyc Pathways resource. We recommend the BioCyc resource for mouse pathway data.
  • We improved the way variants are represented in our non-public-facing database. This is our first step in several planned enhancements related to variants in MGI and The Alliance of Genome Resources.
October 29, 2018
This release offers several new features and updates related to strains. New Strain Detail pages provide basic strain information as well as associated mutations, markers, QTL, phenotypes and diseases. For strains with SNP data, Strain Detail pages offer a new MGI feature, a SNP Profile Heat Map which displays SNP densities and allows you to launch a SNP query from the strain page. For an example, see the A/J Strain Detail page.
The MGI Quick Search field supports strain searches and a new Strain Query, permits limiting your search to strain attributes, such as inbred, congenic, Robertsonian, and wild-derived.
Gene Detail pages now have a new section, Strain Comparison, which allows you to download genomic sequences for 19 mouse strains or forward selected strains to the Multiple Genome Viewer (MGV) to compare chromosomal regions and synteny blocks for the region around the gene.
MGV shows corresponding regions of the selected genomes as horizontal stripes and the equivalent features in each genome via vertical connectors. The navigation of the genomes is synchronized as you scroll in 5' or 3' directions. The Viewer permits searches by genes and other genome features, genome coordinates, and function, phenotype, disease, and pathway terms. You also have the option of sending selected strains to the Sanger SNP Query. The C57BL/6J annotations are from MGI curation and the other 18 strain annotations are from the Sanger Mouse Genomes Project.
Also new to Gene Detail pages, Transcription Start Sites from the Fantom 5 project are now associated with genes and the coordinates to the TSS regions are available from the page. You can also view these features in JBrowse. As an example, see the Gata4 Gene Detail page.
We updated the Mouse SNP Query to allow you to select more than one reference strain, so you can now compare sets of strains. When your search designates a reference strain, new filter options allow you to filter by allele agreement. We also make it easy to select the DO/CC Founders or the Sanger MGP strains.
We added a new section to the Phenotypes, Alleles & Disease Models Search form. You now have the ability to limit your search to the Molecular Mutation type, such as Duplication, Nucleotide repeat expansion, Single point mutation, and translocation.
September 24, 2018
The Multiple Genome Viewer (MGV) allows you to explore and compare chromosomal regions and synteny blocks between the C57BL/6J reference genome and 18 other mouse inbred strains: 16 sequenced and annotated by the Wellcome Institute Sanger Mouse Genomes Project and two (CAROLI/EiJ and PAHARI/EiJ) published by Paul Flicek and Duncan Odom and others, as well as the C57BL/6J reference genome. Currently only the C57BL/6J annotation is “reference quality.” The C57BL/6J annotations are from MGI curation (Y. Zhu et al. ). For GFF downloads, see our weekly reports.
The Viewer shows corresponding regions of the selected genomes as horizontal stripes and the equivalent features in each genome via vertical connectors. The navigation of the genomes is synchronized as you scroll in 5' or 3' directions. The Viewer permits searches by genes and other genome features, genome coordinates, and function, phenotype, disease, and pathway terms. All searches query for canonical genes in MGI's MouseMine. You can forward lists of features to MouseMine and download genomic, coding and exon sequences for a selected feature for designated strains. You can also run an MGI SNP query for strains and a region of interest, and find QTLs that overlap a defined region.
You can access the viewer from the Analysis Tools menu in the dark blue banner at the top of MGI web pages. It will be further integrated into MGI in the next database release.
September 7, 2018
MouseMine now includes genomic data for 18 more mouse inbred strains: 16 sequenced and annotated by the Wellcome Institute Sanger Mouse Genomes Project and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) published by Paul Flicek and Duncan Odom and others, as well as the C57BL/6J reference genome. Currently only the C57BL/6J annotation is “reference quality.”
In your MouseMine search results for a gene or list of genes, several query templates are automatically run. Four in the Genome section of your results include the new data (Example ):
  • Canonical gene --> CDSs in specific strains
    • A report of the coding sequences for each strain for the genes in your list
  • Canonical gene --> Exons in specific strains
    • A report of the exons for each transcript for each strain for the genes in your list
  • Canonical gene --> Strain-specific IDs, biotypes, and locations
    • A report of the genomic sequences for each strain for the genes in your list
  • Canonical gene --> Transcripts in specific strains
    • A report of each of the transcripts for each strain for the genes in your list
Use the Export button above a report to get your results as a tab or comma-separated file, or as FASTA or GFF3 features. Or click on an identifier to get an individual sequence.
August 21, 2018
The GXD Home Page has been redesigned to make it more intuitive and effective. Graphical tiles provide a quick overview of and access to GXD's search functions, including direct access to each of the three (tabbed) search modes of the Gene Expression Data Query Form. A Highlights section alerts users of newly added features and data.
May 7, 2018
The capabilities of the Differential Expression Search have been expanded. This search allows users to query for genes expressed in some anatomical structures and/or developmental stages but not in others. The new feature allows users to search for genes that have been shown to be expressed in a specified structure (or its substructures) and/or developmental stage(s) but nowhere else.
We have developed interface utilities that allow users to compare gene expression and phenotype data for a given gene. The new Gene Expression + Phenotype Comparison Matrix, accessible from gene detail pages, visually juxtaposes tissues where a gene is normally expressed against tissues where mutations in that gene cause abnormalities. The anatomy axis of the view can be expanded and collapsed, allowing users to interactively explore correlations between gene expression and phenotype at different levels of detail. The Mouse Developmental Anatomy Browser has been enhanced; in addition to providing access to expression data for a given anatomical structure, it now provides access to corresponding phenotype data. On Allele Detail pages we have added links to anatomical structures affected by the mutations and links to wild-type expression data for these structures. As well, links have been added to the term detail section of the Mammalian Phenotype Browser, allowing users to access wild-type expression data in tissues associated with the phenotype.
New interface utilities have been developed to help users find recombinase (cre) reporters with activity in specific tissues. The Recombinase (cre) Activity Search now allows users to narrow their query to reporters whose activity has been detected in the specified structure (or its substructures) but nowhere else. Further, a Matrix View that juxtaposes the endogenous expression pattern of a gene against activity patterns for recombinases driven by the mouse gene promoter is now available. The matrix view is accessible from relevant gene and allele detail pages, as well as from the recombinase allele search summary.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
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last database update
10/08/2019
MGI 6.14
The Jackson Laboratory