RNA-Seq Data Analysis    ◾    199

values=c(1,0,-1),

col=c(“red”,”black”,”blue”),

legend=”topright”)

dev.off()

The MD plot in Figure 5.25 shows upregulated (red color), downregulated (blue color), and

nonsignificant gene (black color) in log-fold change versus average log cpm (abundance)

plain. The points are usually dense when all chromosomes are investigated. Remember

that for the sake of simplicity, we demonstrate the differential analysis of gene expression

in a single chromosome (chromosome 22). Both upregulated and downregulated genes are

affected by the condition studied. That suggests that they may have a role on the condition

or the effect may be due to the condition. In this example case, the upregulated and down-

regulated genes may have implications for the breast cancer. These genes can be singled out

and studied to know their roles in the condition.

We can also use the volcano plots to display the differential gene expression results.

A volcano plot is a scatterplot that shows the p-values versus the fold changes in gene

expression. It enables a quick visual identification of genes with large fold changes that

are also statistically significant. In a volcano plot, the upregulated genes are shown toward

the right, the downregulated genes are shown toward the left, and the most statistically

FIGURE 5.25  MD plot showing upregulated (red), downregulated (blue), and nonsignificant

(black).