MGI (Mouse Genome Informatics)

The Gene Expression Profile Search has been Redesigned and Enhanced!

The GXD Expression Profile Search (https://www.informatics.jax.org/gxd/profile) is a tool to search for genes by their expression profile. We have redesigned and enhanced this utility to make it more versatile, improve its search speed, and include access to RNA-seq data.

More versatile searches: Users have always been able to define the expression profile of interest by specifying up to 10 anatomical structures and whether expression is present or absent in these structures. Now users can also specify the developmental (Theiler) stage(s) of interest. They can define search profiles based on developmental stages alone or they can use combinations of anatomical structures and developmental stages. The addition of this functionality to the profile search allowed us to retire the Differential Expression search as all its utilities (and more) are now available in the redesigned Expression Profile search. Read more: https://www.informatics.jax.org/mgihome/news/whatsnew.shtml .

Mouse Gene Expression Data Search You can restrict your query to specific Theiler Stages for each structure specified. You can also query for stages without specifying a structure. NOTE: that when you toggle this button, previous stage specifications (if any) are discarded.

The Gene Expression Database (GXD) is featured this week by the Global Biodata Coalition:

The Gene Expression Database (GXD) What kind of data does this resource provide ? The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehen

The Node, the community site for and by developmental biologists, has a blog post featuring the Gene Expression Database (GXD):

Featured Resource: Gene Expression Database (GXD) - the Node Find out more about the Gene Expression Database (GXD), a community resource that collects and integrates mouse gene expression data generated by biomedical researchers worldwide.

Webinar: An Introduction to the Alliance

The Alliance of Genome Resources will present the first of a series of webinars of approximately 30 minutes.

On September 19, 2024. Noon EDT, Carol Bult will present An Introduction to the Alliance. This will cover searching the Alliance, Gene pages, and Disease pages, and will include a Q & A session.

Register here by September 18 to receive the Zoom URL:

Alliance Event Registration Please click the link to complete this form.

MGI has a new weekly report of Mouse Protein Coding Genes having one-to-one Orthology with Human Genes, the HOM_ProteinCoding.rpt: https://www.informatics.jax.org/downloads/reports/index.html

This report uses homology class data from the Alliance of Genome Resources. There are currently 16,472 genes in this report.

MGI SNP data increased 4-fold.

MGI increased its SNP records 4-fold to over 66 million. These data include the Sanger MGP (v5) SNP set. Use our preeminent SNP Query (https://www.informatics.jax.org/snp) to search for SNPs by gene symbols or chromosomal regions across 101 mouse strains. Search results are limited to 100,000 SNPs (displayed or downloaded), and filters are available to refine search results that exceed the return limit.

To query this large data set efficiently, we implemented the search with Elasticsearch, which allows large data sets to be queried in parallel and improves search speeds. We plan on using this search for other large data sets in MGI/GXD.

In order to update the SNP coordinates to GRCm39 we temporarily lost the dbSNP function classes, such as whether the SNP is in an intron or coding region, and therefore, the Function Class filter in a SNP summary report is limited to "within coordinates of." A future release will provide more function classes. The function classes for individual SNPs can be found by searching the Alliance of Genome Resources (https://www.alliancegenome.org) with the RefSNP ID, one ID at a time. For queries that specify one or more Reference strains, MGI's Allele Agreement filters restrict results to SNPs with strain allele calls that agree or differ from reference strain alleles.

Please send questions and comments to [email protected]

Improving laboratory animal genetic reporting: LAG-R guidelines

The LAG-R framework (Laboratory Animal Genetic Reporting) has just been published in Nature Communications (https://doi.org/10.1038/s41467-024-49439-y). The LAG-R framework is a set of guidelines to support more complete documentation of the genetic make-up of animals that are used in research, with the aim of bolstering reproducibility, reliability, and overall scientific rigor.

The journal Genetics published recent MGI updates:
Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse.

Genetics. 2024 May 7;227(1):iyae031: https://academic.oup.com/genetics/article/227/1/iyae031/7635261

PubMed: https://pubmed.ncbi.nlm.nih.gov/38531069/

Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse Abstract. Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational inves

We removed two features from Marker Detail pages:

We deleted the Interactions section with interacting microRNAs and its linked Interaction Explorer. Instead, for a marker's molecular and genetic interactions, follow the Alliance gene page link in the top, Summary section, of Marker Detail pages.

Also no longer present on Marker Detail pages are the GBrowse thumbnails of the marker region. These were found in the Location & Maps section and linked to JBrowse. The text link ("View this region in JBrowse") remains.