Extended Data Fig. 4: Single-ligand perturbation experiment scRNA-seq quality metrics and cNMF modules.
From: Scalable, compressed phenotypic screening using pooled perturbations
a. Violin plots of the number of UMIs, the number of unique genes, and the percent of mitochondrial genes in the single-ligand scRNA-seq dataset. b. Heatmaps visualizing the Pearson correlation across cells for their module scores of single-ligand cNMF gene expression programs and their scores for existing gene signatures. c. Heatmap of the top three genes by gene spectra score for the single-ligand cNMF modules that corresponded (correlated highly) with the highly variable compressed cNMF modules. d. Heatmap visualizing the Pearson correlation between compressed screen cNMF GEPs gene spectra scores (rows) and single-ligand cNMF GEPs gene scores (columns). e. Ranking of top 50 genes in compressed screen (CS) PDAC IL-4/IL-13 response GEP (top) and single-ligand PDAC IL-4/IL-13 response GEP (bottom) by gene loading values from respective cNMF runs. Genes common to both are highlighted in orange. f. Heatmap depicting regression coefficients for the single-ligand validation data using the single-ligand screen cNMF GEPs as response variables. g. Heatmap depicting regression coefficients for the single-ligand validation data using the CS cNMF GEPs as response variables instead of the single-ligand experiment cNMF GEPs.
