Fig. 2: SCENIC+ analysis on peripheral blood mononuclear cells.
From: SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
a, t-SNE dimensionality reduction of 9,409 cells based on target gene and target region enrichment scores of eRegulons. pDC, plasmacytoid dendritic cell; cDC, conventional dendritic cell. b, Top: distribution of the number of regions linked to each gene. Bottom: distribution showing whether the nth closest region to the target gene has the highest region-to-gene importance score. c, Heat map/dot-plot showing TF expression of the eRegulon on a color scale and cell-type specificity (RSS) of the eRegulon on a size scale. Cell types are ordered on the basis of their gene expression similarity. d, Overlap of target regions of eRegulons. The overlap is divided by the number of target regions of the eRegulon in each row. fr., fraction. e, Visualization of the eGRN formed by EBF1, PAX5, POU2AF1 and POU2F2. TF target nodes are restricted to highly variable genes and regions. f, Aggregated ChIP-seq signal of EBF1, PAX5 and POU2F2 in GM12878 on target regions of either EBF1, PAX5 or POU2AF1 and combinations of two of these factors. g, Chromatin-accessibility profiles across cell types and ChIP-seq signal together with peak calls of EBF1, PAX5 and POU2F2 in GM12878 on chr10:96226082–96316945. Region–gene links are shown as arcs. Region–gene gradient-boosting machine feature importance scores are encoded as colors (from light to dark blue). Predicted target sites of eRegulons are shown using colored ticks and semi-transparent boxes.
