The Ringwald Lab

Our research focus

Our focus is the continued enhancement of the Gene Expression Database for Mouse Development (GXD), a large and well-established resource for the biomedical research community.

As a mammalian organism, the mouse is closely related to human and readily amenable to genetic, molecular, and phenotypic analysis. Researchers combine different types of expression assays to determine the transcripts and proteins generated from each gene, where and when these gene products are expressed, and how their expression varies in different mouse strains and mutants. Further, they correlate expression information with genotypic, anatomical, and phenotypic information to elucidate the molecular pathways of development and disease.

GXD was developed to support these objectives. It integrates different types of expression data, with a particular focus on endogenous gene expression in mouse development. Data from RNA in situ hybridization, immunohistochemistry, knock-in reporter, RT-PCR, northern and western blot experiments are acquired through curation of the published literature and collaborations with large-scale data providers. Selected sets of RNA-seq data are imported from EBI’s Expression Atlas, further processed and annotated, and seamlessly integrated with the other expression data in GXD. In addition, we identify all RNA-Seq and microarray experiments in GEO and ArrayExpress that report on endogenous gene expression in embryonic and adult mice, annotate the metadata for these experiments in standardized ways, and provide a searchable index that helps investigators to quickly and reliably find data sets of interest.

The time and space of gene expression, and the tissue source of RNA-Seq and microarray samples, is annotated using the Mouse Developmental Anatomy Ontology (EMAPA). Initially developed in collaboration with our colleagues from the Edinburgh Mouse Atlas project, GXD has been the primary curator of this ontology for many years and continues to improve and expand the ontology. Based on our work on the Adult Mouse Anatomy (MA) Ontology, we have extended the Mouse Developmental Anatomy Ontology into a continuous system covering developmental and adult stages of mouse anatomy. Both the developmental and adult mouse ontologies have become important standards for describing and integrating biological data that relate to mouse anatomy.

GXD is an integral component of the Mouse Genome Informatics (MGI) resource. Therefore, the expression data are combined with all the genetic, functional, phenotypic, and disease-related information in MGI. This close integration with other data types increases the utility of GXD because the expression data can be queried and analyzed in a larger biological context, thereby facilitating insights into the molecular mechanisms of development, health, and disease.

Visit GXD at https://www.informatics.jax.org/expression.shtml.