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Fig. 5 | Genome Biology

Fig. 5

From: HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

Fig. 5

Biological interpretation of HVRs and LVRs. a For each gene set, the number of significant GO terms is plotted against the p-value cutoff used in the GO enrichment analysis. Significant proximal HVRs/LVRs used here are defined based on the LUAD H3K27ac ChIP-seq data set. b Example GO terms enriched from the genes linked with the significant proximal LVRs. Additional file 3: Table S1 gives a full list of the top 20 GO terms. c, d Box plots showing the fractions of conserved bases in different genomic regions. Here, the conserved bases are defined as those with a phastCons score over 0.9. Red dotted lines indicate the genome-wide fraction. e Example GO terms enriched from the genes linked with the significant proximal HVRs. Additional file 3: Table S2 gives a full list of the top 20 GO terms. f, g Box plots showing the correlations of H3K27ac levels in different regions with the clinical stage of LUAD progression. Here, the correlations are measured by the absolute value of the Spearman correlation coefficient. h Significant proximal HVRs defined for the NSCLC ATAC-seq data set are enriched with somatic SNVs. We have performed 1000 times of random simulation. In each time, a set of proximal peak regions matching the number of the HVRs has been randomly selected. i Significant distal HVRs are enriched with somatic SNVs as well

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