TranSMART now supports the use of Gene Expression and other high dimensional data in the Comparison and SummaryStatistics tabs.
HiDome is an update to the code in the transmartApp application and is automatically included.
No new configuration parameters are needed. Any high-dimensional data should be usable with the new functionality.
When building cohorts in the Comparison tab, a high-dimensional data node can now be dragged into a query box.
Example: For study Breast_Cancer_Sorlie_GSE4382 drag the Breast expression node into a query box
A pop-up window will prompt for a query for a single value in the high dimensional data, for example for the expression of a gene.
Example: Select "Gene Symbol" (only one choice) and choose one of the three value options "Log intensity", "Raw intensity" or "Zscore", then start typing a gene name: BRC. Only genes annotated for the platform will be available for selection.A histogram will appear with the range of expression values, and a count of the number of individuals with expression data for that gene. You can use the slider, or type values in the boxes to select a range of values, or leave the defaults to select all individuals with expression data for your chosen gene.
Queries can be saved for later reuse, in the same way as queries using only clinical data.
Grid View Tab
In the GridView tab you can see the expression values for the individuals selected - for the gene and for the value type you selected.
Summary Statistics Tab
In the SummaryStatistics tab you can see statistics for the gene expression data values (assuming you used expression data in your query.
You can also drag an expression node for a study into the Summary Statistics tab and see expression data displayed for individuals already in your cohort. If you select an entire study you can use this to explore expression data for a selection of genes. The statistics for each gene will be displayed in the SummaryStatistics.