Figure 1.

Illustration of different enrichment measures based on a small region of GO DAG. The full list of genes (F) are denoted as lowercase letters; the genes in set D are marked by boldface. The rectangles contain the subset of genes annotated by each node. Under each rectangle, the first row lists (g_j, n_j) and the P-value presented in P(). The second row lists ( $g_j^{\ast },n_j^{\ast }$) and the B-value presented in B(). In the third row, the parent-child P-value (Grossmann et al., 2007) is presented in G() and the elim P-value (Alexa et al., 2006) is presented in A(), and the posterior probability under MGSA (Bauer et al., 2010) is presented in M(). Note that stronger enrichment is indicated by greater values of B(·) and M(·), and smaller values of P(·), A(·), and G(·).