Fig. 5: Genes induced by IL-4 in BL/6 TRMs exhibit a stronger association with the boundaries of TADs identified through Hi-C analysis. This association is characterized by higher gene expression values and lower expression variability. | Nature Communications

Fig. 5: Genes induced by IL-4 in BL/6 TRMs exhibit a stronger association with the boundaries of TADs identified through Hi-C analysis. This association is characterized by higher gene expression values and lower expression variability.

From: Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically

Fig. 5

a Venn diagram illustrates the genome-wide co-localization TADs identified by Hi-C analysis in both strains. b Hi-C maps from TRMs of BL/6 and BALB/c mice exhibit a representative TAD region that differs between strains (25 kb resolution; raw count map). The grey line indicates the promoter region of the Chil3 gene, and the yellow square indicates the TAD region from Hi-C data. c Dot plots display the distance of the promoter regions of strain-specific induced genes to the TAD boundary region (left). The strain-specific induced genes are identified by DESeq2 in Fig. 1f. Only genes meeting the threshold of FDR ≤ 0.05 (2006 in BL/6 and 1205 in BALB/c mice) are used. Differential genes between BL/6 and BALB/c at the basal level were identified using the EBSeq method with the threshold of FDR ≤ 0.05 (right). The TAD boundaries are defined in the methods and materials section. Asterisks (****) indicate p-values < 0.0001. p-values were calculated using an unpaired t-test, two-sided. Data are presented as mean ± standard deviation. d Scatter plots displaying the RNA expression levels of strain-specific induced genes (2006 in BL/6 and 1205 in BALB/c mice) with corresponding p-values placed at the top of the figure. Asterisks (****) indicate p-values < 0.0001; Asterisks (*) indicate p-values = 0.0105. p-values were calculated using a two-sided unpaired t-test. e Bar plot showing the FANO factor number on strain-specific induced genes (2006 in BL/6 and 1205 in BALB/c mice). f Cluster visualization analysis (WGCNA) was performed on the expression of strain-specific induced genes (2006 in BL/6 and 1205 in BALB/c mice). Light color represents low overlap and progressively darker red color represents higher overlap. Blocks of darker colors along the diagonal are the modules. The gene numbers are labeled at the top of the figure.

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