Figure 2.

Removal of indirect links. As a demonstration, gene X can regulate the expression of both gene Y and Z. But there is no direct regulatory relationship between gene Y and Z. From the calculation of correlation of expression levels of three genes, correlations between gene X and Y, Z are observed as expected. However, genes Y and Z are also significantly correlated since they are both directly regulated by gene X. This correlation from common cause is called indirect link and can be removed by techniques, such as partial correlation, generating a network reflecting regulatory relationships.