Fig. 1

Enhancers mediate up-regulation of immune genes in macrophages upon M.tb infection. a Numbers of differentially expressed genes (DEGs) in infected macrophages vs. macrophages prior to the infection (0 h). b Expression of 1384 up-regulated DEGs. c Expression of 1604 down-regulated DEGs. In (b) and (c), genes are differentially expressed at any time point; expression in TPM was averaged across replicates; dashed lines show median gene expression prior to the infection. d Percentage of genes associated with different number of enhancers in infected macrophages; numbers indicate Fisher’s exact test p-values. e Expression of genes associated with different number of enhancers in infected macrophages; expression in TPM was averaged across infected samples, dashed lines show the median expression of genes not associated with any transcribed enhancer; numbers indicate Wilcoxon two-sided rank sum test p-values. f KEGG pathway maps significantly enriched for up-regulated DEGs with no associated transcribed enhancers, FDR < 0.05. g Top 10 KEGG pathway maps with the lowest FDR enriched for up-regulated DEGs associated with more than two transcribed enhancers. In (f) and (g), next to the bars are the numbers of genes in the KEGG term covered by our gene list; dashed lines indicate FDR = 0.05