Fig. 2 | Nature Communications

Fig. 2

From: Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

Fig. 2

Inferring regulatory relationships between CREs and genes by scCAT-seq. a Overview of three strategies for inferring regulatory relationships. Strategy 1: regulatory links for every gene were assigned when the Spearman correlation of the signal of peaks located at the promoter and distal peaks was above 0.25. Strategy 2: the regulatory links were assigned if the Spearman correlation between the gene expression and the signal of distal peaks was above 0.25. Strategy 3: active transcription factors for every cell were identified by SCENIC, then active regions were identified by matching the binding motifs of active transcription factors to accessible regions. Then regulatory relationships were assigned after applying a Wilcoxon test to determine if the presence of a nearby active accessible region was associated with a significant change in the target gene expression (P-value < 0.05). b Venn plot showing the number of overlapping regulatory relationships identified by the three strategies. c Proportion of ChIA-PET validated regulatory relationships identified by the three strategies in K562 (left), HeLa-S3 (middle), and HCT116 (right) single cells. d, f Heatmaps showing exposure scores of all cells to each signature identified by the NMF clustering of regulatory relationship binary matrices of cell lines (d) and PDXs (f). The exposure score represents the contributions of the signatures to the different samples. e, g Regulatory relationships for the indicated genes in single-cell groups of the cell lines (e) and PDX2 (g). Each panel contains three tracks: the top track shows the regulatory relationship between one peak and the gene (linking them with an arch), where the height and color of the arch show the proportion of cells that share the regulatory relationships; the middle track shows the genomic location of the gene and the associated peaks, where the color of the gene shows the mean expression in each cell type; the bottom track shows the accessible states (on and off) for each peak in each single cell

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