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Gene sets and signature scores
Learn how you can create and save multiple lists of genes as a gene set, visualise the gene set signatures on the platform.
Create and save a new gene set
From the explorer page, you can create and save multiple lists of genes as a gene set on the platform. This can be used to view the expression of the gene set on the main scatter plot with the UMAP, dotplot and feature scatter plot.
Steps
1. From the explorer page, open the Gene sets panel from the options at the top of the page.
2. When you have a list or set of genes, you can create and save a new gene set which can be viewed on the main scatter plot.
3. You can copy and paste a list of genes in the textbox or import the list as a csv file. Here we are creating a new gene set with pasting a list of genes. Make sure give the list a meaningful or descriptive name.
4. Once the gene set has been created, you can view it on the main scatter plot. Use the eye icon to view the gene set on the main plot.
Signature scores
For each gene set created, the gene set signature scores can be download as a csv file. This aggregate signature score is the average expression of the listed genes in the gene set. z-scores are calculated for each listed gene for normalization, then the average of these genes are calculated for each cell. When visualising the gene set on the main scatter plot for UMAP, higher scores are shown in higher saturation in blue by default.
💡Tips!
You can also use the gene set in dotplot, feature scatter plot and you can search the name of the gene set under the feature search bar.Gene sets can be a useful tool to view marker genes in the annotation process of your clusters or identify specific groups of cells.
