Fig. 2: Differential expression and accessibility analysis of cocaine use disorder and GO overrepresenation.

A Heatmap depicting differentially expressed genes identified using a two-sided Wilcoxon rank sum test (Bonferroni-adjusted p < 0.05, log2FC > 0.5, expressed in at least 25% of cells), red = upregulated in CocUD, blue = downregulated in CocUD, top ten DE genes per cell type are labeled. Upset plot depicting the number of shared and distinct differentially expressed features per cell type, for B differential expression and C differential accessibility. D emapplot depicting the top 14 category results of the Gene Ontology overrepresentation analysis for DE genes in a cell type-specific manner. Each circle represents one GO term as a pie chart, indicating the strength of enrichment in the different cell types, represented by color. Edges indicate semantically similar GO terms, with overlapping genes. Circle size indicates the number of genes in the pathway. Overrepresentation was determined using a Fisher’s exact test and Benjamini-Hochberg adjustment for multiple testing. E emapplot depicting the top 14 category results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) overrepresentation analysis for DE genes in a cell type-specific manner. Each circle represents one GO term as a pie chart, indicating the strength of enrichment in the different cell types, represented by color. Edges indicate semantically similar GO terms, with overlapping genes. Circle size indicates the number of genes in the pathway. F heatmap showing differentially accessible (DA) peaks identified using a two-sided Wilcoxon rank sum test (Bonferroni adjusted p < 0.05, log2FC > 0.25, expressed in at least 5% of cells), red = upregulated in CocUD, blue = downregulated in CocUD. G Annotation of DA peaks to their genomic location. H comparison between genomic location of DA peaks to the genomic background, using a two-sided chi-square test with Bonferroni adjustment for multiple testing, *** = p < 0.001, ** = p < 0.01, * = p < 0.05.