Calculate enrichment scores for gene sets from the MSigDB
Over-representation analysis can be used to identify biological pathways or gene sets of interest by determining if a particular set of genes is over or underrepresented in your dataset. This analysis uses counts for the genes within the dataset. The gene set collections that you'll be able to choose from come from MSigDB.
This analysis type is available for single cell RNA-seq experiments in Pluto.
Run an over-representation analysis in Pluto
Before running an over-representation analysis, you need to run a differential expression analysis in your single cell RNA-seq experiment before this analysis type is enabled. For over-representation analysis, each plot will only output values for the cluster comparison you select and the specific gene set you are interested in.
Add an analysis and choose "Over-representation" which will take you to the window to choose which gene set you want to look at and the clusters you want to compare. You can also customize the thresholds to adjust which genes are included in your analysis. Then, select "Run Analysis".
Once your analysis is finished running, you can customize the appearance of your plot in the "Plot" tab. Here you can adjust the plot subtitle, transpose the x and y axis, adjust the number of gene sets shown on the plot and change the colors used in the legend.
