Fig. 5.

CAMERA gene set testing of immunologic gene sets in MSigDB C7. Differential gene expression testing for CIN3 versus CIN1/CIN2 (green column), cancer versus CIN3 (pink column) and K14E7 versus C57BL/6 (black column) were performed using LIMMA. The Empirical Bayesian t-statistics from the analysis was used for the ranking of genes in each comparison for CAMERA gene set testing. The significance value of the CAMERA gene set test, Log10 transformed false discovery rate (FDR) adjusted p-values, for each gene set are plotted along the viridis colour scale (purple, blue, green to yellow) in each bubble as well as on the x-axis where the direction regulation of the of the gene set (up or down; +1 or −1) is multiplied to the significance value. The size of the bubbles correspond to the proportion of genes that are up or down-regulated in each gene set calculated by ROAST where up-regulated pathways were plotted with proportion of up-regulated genes and vice versa. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)