Differential gene expression analysis

In this section, we will cover the steps required to run a differential gene expression analysis on the platform and walkthrough the results from the analysis.

Prerequisite

Before starting the gene expression analysis, you will need at least two saved selections of cells to compare.

Learn more on selecting and saving cells: Cell Selections and Custom Categories

Steps

1. From the explorer page, open the differential gene expression panel from the top of the page.

2. Choose the saved selections for the analysis from the dropdown list and start the analysis with the Compare button

_{💡 You can also create a more complex design of analysis by creating specific selection of cells under a combination of different conditions or classifications.}

3. Once the analysis has been successfully started, you can track the progress from the Ongoing tasks cloud icon in the upper right corner of your page.

‍

Results table and volcano plot

The completed analysis will provide a results table of the differential expressed genes for each group including scores and fold change values, etc. The results can also be visualised in a volcano plot, with options to label the genes on the plot and downloading.

Details

Results table

The table will show the differentially expressed genes sorted by the highest score by default. The selection in which these genes are highly expressed is indicated by the name of the selection at the top of the table. You can change the selection used in the analysis to view their list of genes.

_{💡 The scores in the table are calculated in the same way the marker scores are calculated for each cluster. Learn more about marker scores from: Marker Interpretation.}

Volcano plot

The results can also be visualised on a volcano plot. Genes of interest can be searched for and labelled on the plot.

‍

‍