Fig. 2

Single-cell gene expression inference from chromatin accessibility in developing human brain. A Cell-wise Pearson correlation (y-axis) of inferred and measured gene expression by different methods (x-axis): CMOT (p = 25%, 50%, 75%, 100%), Seurat, MOFA + (Additional File 1: Table S1-S4). See Additional File 1: Fig. S1 A and Additional File 1: Supplementary Methods for additional benchmarking. B Gene-wise correlation between the inferred and measured gene expression, comparing CMOT (y-axis) with MOFA + and Seurat (x-axis). Dots: Genes; Numbers: numbers of genes with improved inference by comparing methods. P-values are from one-sided Wilcoxon rank-sum tests. C Gene-wise AUPRC of cell type marker gene for classifying the cell type. Dashline: baseline = 0.1 (see the “Methods” section). D The measured (x-axis) versus inferred normalized expression (y-axis) of genes (dots) for one cell across four cell types: nIPC/GluN1(first), E.C./Peric. (second), IN (third), R.G. (last). E Heatmap showing different enriched terms ranked by -log10(adj. p-value of enrichment) values for the top 100 highly predictive genes within each cell type (see the “Methods” section). r is the Pearson correlation coefficient. p is the correlation p-value