FIGURE 1.

Differential expression vs. differential co-expression. As a toy example, we consider the expression of four genes in (A) nine healthy individuals and (B) nine individuals with a disease. In this example, none of the genes are differentially expressed, as they have a similar average expression level in both healthy and disease individuals, shown in examples (C) gene G1 and (D) gene G3. However, when we look at the co-expression between genes within healthy individuals (E) and within disease individuals (F), we see that there is obvious differential co-expression between genes in healthy individuals, compared with disease individuals.