Supplementary Figure 2 : Including cCREs at multi-mapping loci identifies promoters for recently duplicated genes

Supplementary Figure 2 | Including cCREs at multi-mapping loci identifies promoters for recently duplicated genes

a, Barplots depicting the percentage of genes with annotated promoter cCREs. Genes are stratified based on GENCODE annotations (top) or classification by Archarya et al.66. Promoter cCREs are stratified by whether they arose from uniquely mapping cCREs (dark red) or multi-mapping cCREs. b, Barplots showing the proportion of genes originating from from whole genome duplication (gray) or more recent small scale duplication (blue) as annotated by Archarya et al. All annotated genes are shown (top) along with genes with uniquely mapping promoters (middle) and genes with multi-mapping promoters (bottom). c, Genome browser view of the EIF3C locus with the default unique-mapping DNase (green) and ATAC (teal) tracks. Multi-mapping DNase-seq signal is shown in black along with DHSs called from this signal. Umap S100 mappability tracks are shown in blue and multi-mapping cCREs are shown in black. d, Genome browser shot of the EIF3CL locus with the same tracks as defined in c. e, Barplots depicting the percentage of multi-mapping cCREs (gray), uniquely mapping cCREs (black), or non-cCRE regions overlap repetitive elements stratified by class. Stars indicate statistically significant differences between multi-mapping cCREs compared with unique mapping cCREs and non-cCRE regions based on two-sided Fisher’s exact tests with FDR correction,  *** for p < 0.001 and * for p < 0.05. Full table of p-values can be found in Supplementary Table 3e.