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Fig. 3 | Genome Biology

Fig. 3

From: Population variation in miRNAs and isomiRs and their impact on human immunity to infection

Fig. 3

Stimulus-specific miRNA responses to immune activation. a PCA of log transformed miRNA abundances. Each dot represents a sample, colored according to the experimental condition (gray – non-stimulated, red – LPS, green – Pam3CSK4, blue – R848, purple – IAV). The same color code for conditions is used throughout the manuscript, and light and dark shades indicate European and African ancestry, respectively. b For each condition, number of DE miRNAs that are either up- (light shade) or down-regulated (dark shade). c Number of miRNAs that are differentially expressed (compared to NS) in a single condition or a combination of immune stimulations (*binomial p < 0.001, significance of overlap between stimuli). df Examples of DE miRNAs for the three most frequent patterns of differential expression across stimuli: d miR-9-5p, exhibiting a TLR-specific response; e miR-3614-5p, responding specifically to viral stimuli; f miR-215-5p, showing an IAV-specific response. g For each condition, number of miRNAs where the canonical isomiR is either up- (light shade) or down-regulated (dark shade). h Example of isomiR-level response to IAV for miR-194-5p. miR-194-5p expresses 5 isomiRs that differ in their 3′ end. Violin plots show the expression of miR-194-5p isomiRs at the basal state, after R848 stimulation (as an example of a TLR-ligand), and IAV. The 3 least frequent isomiRs are grouped for clarity. i Distribution of the percentage of targets from frequent isomiRs (> 1% of miRNA reads, RPM > 1) that differ from those of the canonical isomiR, as a function of shifts in the 5′ start site. Only isomiRs that possess the canonical end site were considered here. j Distribution of the percentage of targets from frequent isomiRs that differ from those of the canonical isomiR, as a function of shift in 3′ end site. Only isomiRs that possess the canonical start site were considered here. k Percentage of common non-canonical isomiRs for which > 1% of their targets differ from those of the canonical isomiR, across various bins of isomiR expression. For each bin, isomiRs whose targets are enriched for at least one GO category are shown in red

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