Figure 3

Evaluation scheme for the inferred potential functional modules. Panel A: A group of 18 OGs, representing an average-sized module. To assess the functional coherence of the module, all possible OG pairs of the module (153 pairs, illustrated as purple lines) are matched against a high confidence reference set of OG pairs from STRING. Panel B: The functional network spanned by the reference OG pairs. Pairwise interactions in the network that are matched by OG pairs of the module are marked as blue edges. In contrast, the majority of linkages in the reference network are marked in gray, indicating that they are not matched by any pair from the module. In each case where three module OGs are exclusively connected by two blue edges, we presume evidence for a transitive relationship (green edges), even though the third edge that completes the triangular relationship is not contained in the reference set. Thus, given the 153 tested pairs, the module yields nine verified pairwise interactions, plus four additional (first-order) transitive interactions. Note that in this case, the module covers three connected components in the network. The five OGs marked with red boundaries are part of the largest connected subcomponent, resulting in a coverage value of 5/18 = 27.8%.