Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells

Figure 6

Enrichment of ATAC-seq peaks in regions representing certain genomic features and relationship of ATAC-seq and RNA-seq data. (a) The enrichment of ATAC-seq consensus peaks in different types of genomic regions is shown with bars representing the enrichment of enrichment . (b, c) Genes that were detected on the RNA-seq level and were also assigned to ATAC-seq peaks were ranked using the function based on both RNA-seq and ATAC-seq (using values of the assigned peaks) within a given cell type comparison ((b) GM-CSF+ vs. GM-CSF−; (c) memory vs. naïve). The ranks of genes using ATAC-seq vs. RNA-seq for ranking are visualized for both cell type comparisons; lines indicate FDR cutoff 0.05 in the respective comparison. value represents the probability of observing this or more directional agreement between the two data types by chance, using only genes significantly differential () in both data types. values were calculated by Fisher’s exact test with Monte Carlo simulation. (d, e) Dot plot representation as in (b, c), but using for ranking and visualizing only (assigned) genes that are significantly differential in both data types.

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