Fig. 3

Differentially Expressed Genes in Each Tissue. a. This schematic illustrates how significantly differentially expressed genes were assigned to either the ‘Rio’ or the ‘BTx’ background, based on their locations relative to the breakpoints (see also Fig. 1). b. A Venn Diagram of DEGs separated by tissue, with each circle of the Venn diagram being further subdivided by how many genes were found on each background. Darker shading indicates genes with a Rio background (i.e. genes that are differentially expressed between the 2 genotypes, BUT had the exact same allele in each), while lighter shading indicates genes with different alleles in the 2 lines. c. Significantly enriched GO categories for each tissue type, also subdivided by genetic background. Colors correspond to the categories outlined in panel b. Asterisks denote the significance level (* = p < 0.01, ** = p < 0.001, *** = p < 0.0001). d. The most commonly observed expression patterns over time. The top row shows expression patterns in Rio, while each graph below shows the corresponding expression pattern in PR22. The x-axis is time (or growth stage), while the y-axis is the variance stabilized count of each transcript