Analysis outline. We first apply logic analysis to microarray data to identify gene triplets whose regulation obeys one of the possible logic functions such as the AND function: C is regulated iff A and B are regulated (the functions are described in detail in Additional file 1: Table S1). Next, using a curated set of protein complexes [19, 32], we map gene triplets onto complexes. Finally, we identify triplets of complexes and calculate their significance (see Methods section). The analysis enables us to predict coordinated regulation of these complexes.