Fig. 4

The Volcano plot of differential gene expression tumor vs normal comparison. Genes are plotted in different colors depending their passes of the following filters. Filter 1: the differential expression of gene is statistically significant, ie. p-valve < 1/22277, across all 50 runs; Filter 2: The absolute value of the average log2 fold change across the 50 runs is greater than 2; Filter 3: The average expression level of tumor group or normal group is greater than 6. Green spots represent genes that have passed all the 3 filters and been selected into the gene signature; Black spots represent genes that did not pass filter 1; Red: genes that passed filter 1 but not filter 2; Orange spots are genes that passed filter 1 and 2, but not filter 3. Additionally, a number of top up-regulated genes and down-regulated genes are plotted in darker green with their gene symbol as textual label. These probes are primarily selected by their magnitude of differential gene expression while avoiding label overlaps on the plot