The mouse Gene Expression Database (GXD): 2021 update.

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD\u27s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment

The mouse Gene Expression Database (GXD): 2019 update.

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD\u27s gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities

PhD

dissertationTheiler's murine encephalomyelitis viruses (TMEV) are picornaviruses that can infect the murine central nervous system. There are two subgroups of TMEV based on their biological properties in mice. The Theiler's Original (TO) subgroup contains strains that produce an acute polioencephalomyelitis and a chronic demyelinating disease, whereas members of the GDVII subgroup produce a lethal encephalomyelitis. The ability of DA virus (TO subgroup) to produce a demyelinating disease renders this virus infection a model for human demyelinating diseases such as multiple sclerosis. During infection, with members of the TO subgroup there is a shift in tropism from neurons in the gray matter during the acute stage to glial cells in the white matter during the chronic stage of disease. One explanation for the shift in cell tropism is a change in the interaction between virus and the host cell. This thesis describes, as part of the elucidation of virus-cell interaction, the generation and characterization of DA virus mutants that contain specific mutations in the viral capsid protein VP1 at sites that are believed to be important contact sites for the virus receptor. A mutant virus with an amino acid substitution at an exposed site of the virion adjacent to the putative virus receptor binding site exhibited a large plaque phenotype, grew to lower titers in cell lines from tissues of a variety of species, and had a slower replication cycle in vitro. When this mutant was injected intracerebrally into susceptible mice, an altered tropism was found during the acute stage of the disease and virus did not produce a chronic demyelinating disease. The phenotypic difference seen with this mutant virus was not due to a difference in binding or uncoating of virus, but due to a difference in the rate of penetration. In addition, it is shown that permissiveness of cells to TMEV infection can not always be correlated with binding of virus to the cell surface. BSC-1 cells bound high levels of virus but were semipermissive to virus replication. The highly permissive BHK-21 cell line only bound intermediate levels of virus

The mouse gene expression database (GXD): 2007 update

The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, GXD aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. GXD is available through the MGI web site a