Fig. 4: Illustrations of the correlations between ATAC-seq, CHi-C and RNA-seq time course profiles. | Nature Communications

Fig. 4: Illustrations of the correlations between ATAC-seq, CHi-C and RNA-seq time course profiles.

From: Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis

Fig. 4

a Density plots of the Pearson correlation coefficients between ATAC-seq and CHi-C, ATAC-seq and gene and gene and CHi-C under various distance ranges around promoters. Distances ranges include those <5 Mb, between 1 and 5 Mb, between 500 kb and 1 Mb, between 200 and 500 kb and <200 kb. Black lines represent the density plots of the corresponding random background. P values from Wilcoxon tests are labelled in each panel with sample sizes of 27,805, 8229, 4742, 7942 and 6892 for categories < 5 Mb, 1–5 Mb, 500 kb–1 Mb, 200–500 kb and <200 kb, respectively. b Comparison of the log2 fold change between CHi-C and gene data for all data set (upper) and those highly correlated ones with Pearson correlation coefficients between ATAC-seq, gene and CHi-C over 0.5 (lower). c Comparison of the log2 fold change between ATAC-seq and gene data for all data sets (upper) and those highly correlated ones with Pearson correlation coefficients between ATAC-seq, gene and CHi-C over 0.5 (lower). Box plot shows the median, the interquartile range (IQR) and Turkey whiskers (±1.5 times IQR).

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