RNA-Seq data added to GXD

GXD now includes RNA-Seq data. 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. The data sets have been imported from the EMBL-EBI's Expression Atlas. To effectively integrate these data into GXD, we process these files further and annotate the sample metadata. Details…

Add RNA-Seq data to the Standard Search

The GXD Expression Data and Image Search - Standard Search Form has a section for Assay type selection. Click RNA-Seq to include that data in the Summary.

New filters added to search summaries

GXD has added new filters to the gene expression data search summaries. This enables users to quickly and efficiently extract the expression data of interest to them.

Visualization and analysis of RNA-Seq data in Morpheus

By merely clicking a button on the gene expression data search summary, the RNA-Seq data from a GXD search, including the standardized sample metadata annotated by GXD, will be rendered into an expression heat map via Morpheus, a heat map visualization and analysis tool created at the Broad Institute.

Morpheus features include:

• Hovering over any cell will display its value
• Sorting and filtering options allow you to customize the heat map
  • Filters allow you to remove samples (columns) and/or genes (rows)
  • Clicking beside a metadata label will use the values in that field to group the samples
  • Clicking a column (or row) will sort the heat map by TPM values in that column (or row), from high to low; a second click will reverse the order
  • Triple clicking a column (or row) will sort the TPM in alternating groups of 10 of the most similar and dissimilar items, allowing for simultaneous viewing of both ends of the sort
• Create Calculated Annotations can be used to do statistical calculations, such as deriving the mean absolute deviation (MAD) or variance across the TPM values per gene
• Hierarchical Clustering can be used to group samples by similarity
• Nearest Neighbors can be used to find genes/samples that are similar to the genes/samples of interest.