Extended Data Fig. 9: Treatment-dependent cis-regulatory elements and TF-associated genes.
From: Joint single-cell measurements of nuclear proteins and RNA in vivo
a-c. Prediction of co-regulatory patterns by TF motif enrichment in DEGs associated with c-Fos or p65 (additive model), or their interaction c-Fos*p65 (interaction model). a,b. Significance (-log10(P-value), y axis) and rank order (x axis) of TF motifs (dots) enriched in enhancers of DEGs associated with each protein (additive model) or protein-protein (interaction model) term in excitatory neurons, using enhancers of PBS (a) or KA (b) treated sample as background. Black: significant motifs (P < 10−3, hypergeometric test); gray: not significant. c. TF motif enrichment (columns; dot size, -log10(P-value)) and proportion of excitatory neuron nuclei expressing the RNA (color) of significant TFs (rows) in the enhancers of c-Fos (additive model), p65 (additive model), or c-Fos*p65 (interaction model) DEGs, compared to other enhancers within the KA treated sample. d. Treatment-dependence of gene association with c-Fos and p65. Global effect size of genes (dots) associated with c-Fos (left) and p65 (right), after PBS (x axis) or KA treatment (y axis) (Methods). Colored dots: genes with significant coefficients (Benjamini-Hochberg FDR < 5%) in PBS (gray), KA (green), or both (black). Select genes are labeled. Bottom right: linear correlation R2 and associated P value (two-sided t-test).
