Fig. 3: Results from scMultiMap on single-cell multimodal data from postmortem brain samples in ref. ³⁶.

a Empirical type I errors on permuted data for 1000 randomly selected peak-gene pairs. Normalized peak values were randomly permuted within subject to break dependency with gene expression while preserving variations among subjects. The dashed line marks the nominal level of 0.05. Boxplots display the median (center), the first to the third quartiles (box), and whiskers extending to values within 1.5 × the distance between the quartiles. Points indicate outliers beyond this range. b Precision-recall curves on simulated data. See color legend in (a). c Consistency of significant pairs (BH-adjusted p-value  <0.2) with enhancer-gene pairs measured by PLAC-seq³ in excitatory neurons (Exc), inhibitory neurons (Inh) and oligodendrocytes (Oli) (Methods). See color legend in (a). d, e Reproducibility of significant pairs with independent single-cell multimodal data on brain samples from³⁹ across cutoffs of BH-adjusted p-values, as evaluated by the enrichment (d) and the number (e) of reproduced counts. In c–e enrichment is quantified by odds ratio (OR) and log OR in (c) and (d) respectively (OR=0 not shown), and p-values are from one-sided Fisher exact tests. f, g Enrichment of GO biological processes among the target genes in trios identified for each TF in excitatory neurons (f) and astrocytes (g). Color intensity is given by BH-adjusted -\({\log }_{10}p\)-values from one-sided Fisher exact tests (values larger than 10 were set to 10). Source data are provided as a Source Data file.