They enable users to use gene function, phenotype and disease ontology annotations, as well as marker type, to filter expression assay results. These filters have been added to the gene expression data search summaries. GXD has developed new filters that take advantage of the genetic, functional, phenotypic and disease-related information in MGI. New data filters on GXD's search summaries These two steps enable the full integration of these data into GXD/MGI and makes them accessible via existing search tools. We also annotated metadata for the RNA-seq samples using the same controlled vocabularies and ontologies we use for all other expression data in GXD. This binning of TPM values allowed us to assign a detected/not detected value to these data, as is done for all the other expression data in GXD. Using the Expression Atlas thresholds as a guide, the TPM values are assigned to expression bins of high, medium, low, and below cutoff.
To effectively integrate these data into GXD, we processed these files further to compute averaged quantile normalized TPM values per gene per biological replicate set. We chose the Expression Atlas as our data source because their team selects high quality data sets from the public repositories (ArrayExpress and NCBI's GEO) and then uses a standardized pipeline to re-analyze the data, generating consistently processed TPM values. We have integrated these data with the other types of expression data in GXD and with the genetic, functional, phenotypic and disease-related information in MGI and thus made them accessible to many new search capabilities. The data sets have been imported from the EMBL-EBI's Expression Atlas. In keeping with GXD's scope, these data are from experiments that examine endogenous gene expression in wild-type and mutant mice during the embryonic stages and/or postnatal life. GXD has been expanded to include RNA-Seq data. It can be found as a tab on the Gene Expression Data Query. It allows users to define the expression profile of interest by specifying up to 10 anatomical structures and whether expression is present or absent in these structures. GXD has developed the Expression Profile Search, a tool to search for genes by their expression profile. GXD introduces an Expression Profile Search
MGI-Mouse Gene Expression Database (GXD): What's New - Gene Expression Database News
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