Figure 2.

Mouse transcriptome common core. (A) Distribution of log2 fold change across contrasts with significant (FDR < 0.01) DEGs. Dark blue and dark red, respectively, indicate genes that are core down and core up, and pale blue/pale red, respectively, indicate down and up DEG. Pie charts with the same annotation colors show what percentage of each contrast’s DEGs falls into each category. Stacked bar charts with the same annotation colors show each contrast’s DEG quantity. (B) Histograms of significantly up and downregulated genes cut for different FDR thresholds and the number of total contrasts in which a DEG appears. Genes at the extreme ratios of 0 or 1 percent upregulated are highly concordant across contrasts, whereas genes that fall into the middle are discordant. For consistency in this analysis, we inverted the direction of fold change for the four contrasts of the TG model. (C). Genes as annotated by Gencode and condensed into eight broad categories. We considered 53,661 genes from our annotation and found 32,539 that passed our expression filter in at least one contrast. The common core (FDR < 0.01 in at least four contrasts) is comprised of 2971 genes. (D). Exploration of genome location trends in the common core. All non-DEGs are plotted in the upper portion of the panel, and violin plots show areas of gene density. Chromosome 8 was selected for further examination in the lower half of the panel, with baseline genes in equal quantity to the core genes (150) also plotted. CBS method is used to identify trends in the up/down/baseline genes. The bands on middle dot plot show these CBS results, and the lower stack plot shows the density of up, down, and baseline genes on chromosome 8.