How to Obtain Subpopulations Expressing Target Genes After Seurat Clustering and Analyze Specific Genes of Interest?
After performing single-cell clustering with Seurat, you can obtain subpopulations expressing target genes and analyze specific genes of interest in the following steps:
Obtain Subpopulations Expressing Target Genes
First, filter the gene expression matrix from the Seurat object for the genes of interest using your gene list. Functions like FetchData() or SubsetData() in Seurat can help with this. Then, re-cluster the filtered expression matrix to obtain the subpopulations expressing the target genes.
Label Target Subpopulations
Once you have the subpopulations expressing the target genes, use Seurat’s Idents() function to label these subpopulations for easier subsequent analysis.
Gene Group Analysis
For genes of interest, use Seurat’s FindMarkers() function to perform differential expression analysis and identify genes significantly expressed in the target subpopulation. This function compares the target subpopulation to other subpopulations and provides a list of differentially expressed genes with statistical results.
Visualization
For the identified differentially expressed genes, use Seurat’s built-in plotting functions, such as VlnPlot(), DotPlot(), or FeaturePlot(), to visualize and showcase the expression differences between the target subpopulation and other subpopulations.
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