Fig. 5: MultiVeloVAE infers continuous coupling and decoupling factors in differentiating hematopoietic stem and progenitor cells.
a The dynamics of chromatin, unspliced RNA, and spliced RNA for several lineage markers, colored by continuous coupling factors, range from −1 (coupled repression) to 1 (coupled induction). The diverging colormap centers around 0. The inset shows the RNA expression of the marker genes on the UMAP embedded cell states from Fig. 4a. b Similar to a but colored by continuous decoupling factors, range from −1 (kc = 0, ρ = 1) to 1 (kc = 1, ρ = 0). c Scenic + gene regulatory network (GRN) containing all transcription factors (TFs) and genes participated in velocity inference. The TF nodes are labeled with the TF names. Region nodes regulated by the TFs are colored by their differential accessibility on a log2 scale in the specified cell type. The edges linking regions to target genes are colored by accessibility-expression correlations and transparent by region-to-gene importance from Scenic+. The target gene nodes are colored by cell-type-specific mean coupling factors and transparent by the magnitudes. For each cell type (Top-Platelet and Bottom-DC), the activated TF-regulated triplets are circled. d The Spearman correlation coefficients of coupling (Left) and decoupling (Right) factors of target genes with the RNA expressions of the TFs. e The mean predictions and credible intervals of posterior-sampled cells along with a zero line colored by cell types. f Example normalized dynamics plots of a TF's RNA, the associated region accessibility, and the target gene’s chromatin, unspliced, and spliced counts plotted along inferred latent time for specified lineages. Modality counts were reconstructed by MultiVeloVAE. Source data are provided as a Source Data file.
