Over-represented motifs from ChIP data reflect three types of binding mechanisms. A solid arrow means that the TF binds directly to the motif. A dotted arrow means that a motif (for example, M1) is over-represented in TF1 ChIP data. This can occur (a) because of direct binding, or (b, c) because of two modes of indirect binding. (a) M1 is a direct-binding motif of TF1. (b) M1 is an indirect piggy-back binding motif of TF1 via TF2, where TF1 binds TF2, and TF2 binds the motif. For example, M1, TF1, and TF2 could correspond to GTAAACA (the Fkh2 motif), Ndd1, and Fkh2, respectively, as Ndd1 binds to Fkh2, which in turn binds to GTAAACA. (c) M1 is an indirect cross-binding motif of TF1 via TF2. For example, M1, TF1 and TF2 could correspond to GTAAACA (the Fkh2 motif), Mcm1, and Fkh2, respectively, since Mcm1 binds to its own motif (M2) on the same promoter as the Fkh2 motif.