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May 22, 2014
The Phenotypes, Alleles & Disease Models Query Form and the Genes & Markers Query Form have been rewritten and offer superior performance and the ability to sort your results and export them as tab-delimited text.
The Phenotypes, Alleles & Disease Models Query Form has new allele categories that permit refined searches for specific allele types and the option to limit your search to those from specific high-throughput projects and repositories.
Some high-throughput mutagenesis projects, such as those that generate chemically induced mutations, may produce mutations in multiple sites in the genome. In MGI, these incidental mutations are these types of mutations that have been detected via sequencing but have not yet been confirmed or studied. You can now access information on these mutations from the Alleles and phenotypes section of Gene Detail pages.
The Human—Mouse: Disease Connection has new features:
  • You can now search by uploading a text file of gene symbols or IDs.
  • If you search the Human—Mouse: Disease Connection with a VCF file, by default, MGI applies filters to the file. You now have the option of performing an unfiltered search.
  • The form now uses genome coordinates from human build GRCh38, so both human and mouse coordinates are from the latest builds. If your coordinates are from earlier builds, the form links to an NCBI tool that will convert them to the latest build.
March 6, 2014
The Gene Expression Database (GXD) uses the Mouse Developmental Anatomy Ontology to describe expression patterns in a standardized way. This ontology has been significantly improved, and a new anatomy browser has been implemented that is more interactive and provides easier access to anatomy data and associated expression data.
The new version of the Mouse Developmental Anatomy Ontology, developed in collaboration with EMAP, provides an "abstract representation" of the anatomy that specifies anatomical structures together with their developmental (Theiler) stage ranges. This abstract representation is in addition to the previously available stage-specific representations for all Theiler stages. Further, the ontology’s hierarchical organization now allows anatomical terms to have multiple parents (i.e. is a directed acyclic graph). Thus, the anatomy can be represented and searched from multiple perspectives.
The newly developed Mouse Developmental Anatomy Browser allows users navigate through this ontology to locate specific anatomical structures and to obtain associated expression data. This browser contains three interactive sections: search, term detail, and tree view. Searching is aided by an autocomplete list. The tree view allows for the viewing of terms in context, by providing the ability to expand and collapse branches, as well as providing links to associated expression data. The term detail provides information about each term as well as allowing users to toggle between stage-specific and stage-independent instances of terms.
Expression data summaries are returned by the GXD queries and accessed by expression result links on detail pages through MGI. These data summaries now have filters to allow users to further limit their results to specific anatomical systems, assay types, Theiler stages, detection of expression (yes or no), and to wild-type or mutant specimens.
GXD is also pleased to announce that additional RNA in situ hybridization data from the GenitoUrinary Development Molecular Anatomy Project (GUDMAP) database are now available at J:171409. This set now includes over 137,000 RNA in situ hybridization results obtained from embryonic and postnatal specimens, analyzing 3,676 genes in 4,499 assays and accompanied by 10,655 image montages for ~ 32,000 individual images.
Finally, GXD pages within MGI are now demarcated by gold sidebars and/or the presence of a GXD logo.
December 12, 2013
The new Human—Mouse: Disease Connection site provides a path into mouse genetic and comparative data from the human or mouse perspective. Users can begin to explore data by searching for genes (symbols, names, IDs) or genome locations from human or mouse, or by searching with mouse phenotype or human disease terms. Searching also can be done using VCF file input for human or mouse data.
Now, clinical researchers, whose primary focus is on human genetic disease, variants, and mutations, have a new highly-accessible way to explore the mouse genome for experimentally determined models of human phenotypes and diseases; as well as to find potential candidate models where well-characterized, genetically defined mice display a spectrum of phenotypes similar to humans. Likewise, mouse geneticists can readily explore relationships between mouse phenotypes and the human diseases that are associated with mouse mutations.
Any search (by genes, location, phenotype term or disease) returns an initial grid of human/mouse gene homologs x phenotype/disease terms that matches the search parameters specified. Within the grid, colors specify presence of relevant human and mouse data. Each colored cell is an active link leading to more detail. In addition, the grid is only the first of three tabs presented on the result page. Also available are a Genes tab, providing information and links about each human or mouse gene returned by your search, and a Diseases tab, providing information and links about each human disease returned by your search. Data on the Genes and Diseases tabs are downloadable.
This release of the Human—Mouse: Disease Connection site is considered "beta". We will expand its capabilities in the future to include the incorporation of human phenotype terminology using the Human Phenotype Ontology, make more visible connections to mouse resource repositories, include graphical synteny maps to enhance comparative location visualization, and provide for multiple file format uploads for searching. We hope you find this initial release useful and encourage your feedback.
June 20, 2013
GXD has made it easier to view and search for its expression images. An images tab has been added to the GXD search return, allowing users to search for expression images by using all the parameters available on the Gene Expression Data Query Form. Further, these images are now included on the assay detail pages, so they can be viewed together with their annotated results.
The Differential Expression Search, present as a tab on the standard GXD query form, allows biologists to search for genes that are expressed in some anatomical structures but not others and/or in some developmental stages but not others. Formerly named The Gene Expression Data Expanded Query, this tool has been streamlined and clearly delineates the different search capabilities. The mechanisms behind the differential searches have been re-designed to allow for speedier returns and the search return now provides tabbed data summaries that are sortable and interactive.
The Cre Portal is updated with the ability to search for recombinase activity in tissues via an autocomplete search field of structures from the Mouse Anatomical Dictionary. In your search results, it is easier to see in which structures activity was detected or not detected and results can be sorted and columns, rearranged.
Recombinase allele detail pages have an improved summary of driver tissue activity and show both ages and structures where activity was detected/not detected.
On Recombinase allele detail pages a Your Observations Welcome button allows user to submit allele specific recombinase activity data.
MGI SNP data are updated to NCBI dbSNP Build 137 and use the GRCm38.p1 build genome coordinates. MGI now includes over 24,000,000 SNP IDs and almost 16,000,000 refSNPs.
May 16, 2013
MGI is pleased to announce a new implementation of comparative genome data. Previously we used a one-to-one orthology relationship between a mouse gene and that of another mammalian species. MGI now uses homology class data from HomoloGene and supports a "many-to-many" relationship between mouse genes and their vertebrate homologs. Chicken, zebrafish and rhesus macaque homologs are now included in this release as well as human, chimpanzee, dog, cattle and rat.
Vertebrate Homology Class pages include genetic location and links to EntrezGene, Comparative GO Graphs, sequences and HomoloGene multiple sequence alignments. For an example, see this complement component Vertebrate Homology Class page.
Redesigned MGI Human Disease and Mouse Model Detail pages support the new homology class data and link to vertebrate homology class pages and mouse model phenotype data. For an example, see this Systemic Lupus Erythematosus Human Disease and Mouse Model Detail page.
With this release, references now link to curated Gene Ontology (GO) functional annotations, in addition to genome features, phenotypic alleles and expression literature curation. For an example, see this reference summary page.
March 15, 2013
MouseMine represents a new generation of access to MGI data. Powered by InterMine, MouseMine offers flexible querying, numerous predefined query templates, a point-and-click interface for building your own queries or modifying a template, iterative refinement of results, built-in enrichment analysis, downloading in multiple formats, forwarding to Galaxy, linking to other model organism Mines, and more.
  • currently contains genetic, genomic and annotation data (function, phenotype, disease) from MGI
  • offers many useful "canned" queries, plus point-and-click query editing
  • supports links to any object's detail page or to any query results page
  • allows any query result to be downloaded (text, xml, json) or forwarded to Galaxy
  • supports uploading and manipulating lists of objects
  • provides web service access to all of the above functions
January 31, 2013
MGI now integrates phenotype data from high-throughput phenotyping centers with curated data from scientific publications, providing comprehensive comparative phenotypes for mouse mutants. Current data sets include those from the Wellcome Trust Sanger Institute (WTSI) and the Europhenome (EuPh) data. This integration allows specific comparisons between different Center data interpretations and is a model for future MGI data integration from the International Mouse Phenotyping Consortium (IMPC). All data on the MGI website are refreshed weekly.
MGI Allele Summary Pages have been streamlined, concatinating biological systems where phenotypes have been detected while removing the details of each genotype examined. In addition, Allele Detail pages have been redesigned for clarity and performance, and to display results from these high-throughput phenotyping centers. Sex-specific phenotype data also are easier to discover.
For an example, see this MGI Allele Detail page.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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