Supplementary Figure 4: Comparison of number and effects of ASE-SNVs identified in ChIP-seq and ATAC-seq. | Nature Genetics

Supplementary Figure 4: Comparison of number and effects of ASE-SNVs identified in ChIP-seq and ATAC-seq.

From: Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits

Supplementary Figure 4

(a) Number of uniquely mapped reads for each data type and subject (n = 7). Each open circle corresponds to merged reads from different samples of the same subject. (b) Average FrIP across different samples of the same subject in each data type. (c) Median number of reads at all heterozygous SNVs tested for ASE in each individual. (d,e) Scatterplot showing increase in the median SNV coverage as a function of the number of mapped reads (d) and of FrIP (e) in each subject (n = 7). Continuous lines indicate that the relation is significant (linear regression, P < 0.05). (f) Scatterplot showing increase in the fraction of identified ASE-SNV in each subject (FDR < 0.05), as a function of the median SNV coverage. Continuous lines indicate that the relation is significant (linear regression, P < 0.05). (g) Distribution of the mean SNV coverage between subjects, across all SNVs analyzed in each data type (number of SNVs in each distribution from left to right: 30,463, 26,201, 116,898, 123,151 and 19,371). Median values are shown as white dots within the violin plot and are indicated. (h) Distribution of the number of ASE-SNVs (FDR < 10%) in 100 samplings of 100 SNVs with the same coverage in the different data types. (i) Distribution of the mean ASE effect sizes (allele frequencies) of the 100 SNVs samples shown in h. Median values are shown. Boxplot elements: median (thick line), lower and upper quartiles (box), maximum and minimum (wiskers). (j-l) Scatterplot showing correlation of ASE effects of the same SNV between peaks from different data types in iPSC-CMs: (j) NKX2-5 vs. ATAC-seq peaks; (k) NKX2-5 vs. H3K27ac peaks; (l) ATAC-seq vs. H3K27ac peaks. The union of significant ASE-SNVs in each pair of datasets is shown, with ASE effects expressed as the proportion of the reference allele at heterozygous SNVs. Gray dots denote ASE-SNVs significant (binomial test, FDR < 0.05) only in the peaks indicated in the x-axis, blue dots in the y-axis, and green dots in both. Pearson correlation coefficient (r), number of SNVs (n) and P-values are indicated.

Back to article page