Fig. 3: Identifying enhancer-gene regulatory connections in our CRC tissues by ABC model. | Nature Communications

Fig. 3: Identifying enhancer-gene regulatory connections in our CRC tissues by ABC model.

From: Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk

Fig. 3

a The flowchart of ABC model predicting functional variant in CRC tissues, which was created with BioRender.com. b Cumulative fractions of the number of enhancers predicted to regulate each gene (mean = 2.8). c Cumulative fractions of the number of genes regulated by each ABC enhancer (mean = 2.3). d Cumulative fractions of the genomic distances between the enhancer and the gene for each predicted enhancer-gene connection (median=48,375 bp). e Precision-recall plot of the accuracy for assigning genes to regulatory variants that predicted by ABC model or other previous predictions, considering a credible set consisting of 27 variant-gene connections which were validated by functional experiments. Recall indicated fraction of the variants identified, and precision indicated fraction of the target genes that was predicted. f Genomic annotation of ABC enhancers. Pie chart indicates the proportions of ABC enhancers annotated with each positional category. Upset plot displays the number of ABC enhancers between groups for each intersection. g Summary of ABC enhancers in CRC tissues. Plot included 124,474 non-promoter candidate elements in terms of ATAC peaks. The coloring of the heat map represented the fraction of elements in the corresponding distance and activity bins that are ABC enhancers. h Enrichment analyses of ABC variants in regulatory elements compared with non-ABC variants in CRC tissues. P-values were calculated by two-tailed Fisher’s exact test and bars indicate 95% confidence intervals (CIs). i Enrichment analyses of ABC variants in CRC GWAS signals (LD ≥ 0.2). P-values were calculated by two-tailed Fisher’s exact test and bars indicate 95% confidence intervals (CIs). j Enrichment analyses of CRC GWAS signals in ABC enhancers and other regulatory elements. Results were calculated by two-tailed Fisher’s exact test. Error bars represented the 95%CIs. k Quantile–quantile plot of CRC GWAS P values. ABC variants are shown in comparison with genome-wide variants. GWAS variants were binarily annotated using ABC variants. Source data are provided with this paper.

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