Merge differential expression results

Why Merge differential expression results

Plotting fold changes of different data types (mRNA and Protein in this example) together is a common integrative approach in multi-omics studies. By visually examining the scatter plot and specifically looking at the outlier genes, researchers can gain crucial insights into the hierarchy and kinetics of regulation within the biological system being studied. In ICM, this analysis can be performed by running the “Merge Differential Expression Results” task.

Running Merge differential expression results

The task can be invoked on any differential analysis results data node.

• Click a data node of differential analysis such as DESeq2

• Click the Exploratory analysis section of the toolbox

• Click Merge differential expression results

• In the task set up page, push the Select data node button to pick the right option and hit the Select button

• Hit the Next button to proceed

• Select the matching features for each data node

• Click Finish to run

The result is stored under a Merge results node. To open it, double click on the node or select the respective Task report from the context sensitive menu.

Task report

For this task, the report directly opens a 2D scatter plot in Data Viewer. Fold changes of different data types (mRNA and Protein in this example) in log2 scale are labeled at two axes separately. In the example, mRNA fold change reflects transcriptional activity (gene expression at RNA level); Protein fold change reflects translational and post-translational processes. By plotting them together, one can see how changes in mRNA abundance correlate with protein abundance.