Fig. 4

Application of TF and pathway analysis tools on a representative scRNA-seq dataset of PBMCs and HEK cells. a Dendrogram showing how cell lines/cell types are clustered together based on different hierarchy levels. The dashed line marks the hierarchy level 2, where CD4 T cells, CD8 T cells, and NK cells are aggregated into a single cluster. Similarly, CD14+ monocytes, FCGR3A+ monocytes, and dendritic cells are also aggregated to a single cluster. The B cells and HEK cells are represented by separate, pure clusters. b, d Comparison of cluster purity (clusters are defined by hierarchy level 2) between the top 2000 highly variable genes and b TF activity and TF expression and d pathway activities. The dashed line in b separates SCENIC as it is not directly comparable to the other TF analysis tools and controls due to a different number of considered TFs. c UMAP plots of TF activities calculated with DoRothEA and corresponding TF expression measured by SMART-Seq2 protocol. e Heatmap of selected TF activities inferred with DoRothEA from gene expression data generated via Quartz-Seq2