Fig. 4: sciCAN identifies common response after CRISPR perturbation. | npj Systems Biology and Applications

Fig. 4: sciCAN identifies common response after CRISPR perturbation.

From: sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

Fig. 4

a Visualization of single-cell CRISPR-perturbed K562 RNA-seq and ATAC-seq data via UMAP. Cells are colored by identified cell clusters (left) and modality source (right). b Spearman correlation between RNA-seq and ATAC-seq profiles of cells in different clusters in both modalities. Gene expression or gene activity matrix was averaged by cell clusters. c Shared gene signatures of the 3 cell clusters in both modalities. Differential gene activities or expression were identified through ‘Wilcoxon’ test in Scanpy package. d Ranking of sgRNA representation in each cluster (blue = C0, orange = C1, green = C2) in both RNA-seq (left) and ATAC-seq (right) data. Genes perturbed in both experiments are highlighted. e Gene signatures of cells targeted by sgELE1, sgYY1, and sgGABPA in cell cluster 1. f Genes whose activity patterns distinguish cells in cluster 0 and cluster 2 among cells in these clusters perturbed by the same gRNAs.

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