Fig. 5

Example of NIEHS pipeline TE query analysis results from liver vs other tissues (except the ovary, testicle and uterus). A) Box plot of the average expression of TE miRNAs within a tissue displaying the distribution of data based on the minimum, first quartile, median, third quartile, and maximum values. The x-axis is the tissues/organs and the y-axis is the log base 2 of TMM. B) Cluster analysis of the average expression of TE miRNAs (rows) in the tissues (columns). The clustering is performed in R using the heatmap.2 function with default parameters (dist for the distance metric and hclust to perform the hierarchical clustering) and scaling/centering of the data by row (miRNAs). The heat map colors are represented by z-scores as depicted in the legend. C) Bar chart of the average expression of TE miRNAs with the vertical bar representing the standard deviation of the mean. The x-axis is tissues/organs and the y-axis is TMM