Figure 3

Cy3 fluorescent signal distribution of the spot intensity. (A) The rank-ordered signal distribution of the Cbf1 PBM shows a deep leftward slope followed by a heavy right tail because the signal distribution is due to a specific interaction between the protein and features on the microarray. Two independent linear models, y = ax+b, were applied in the deep and the heavy right tail regions. (B) Cy3 intensity was inspected to verify that DsRed was not binding to DNA sequences on the PBM. With the exception of non-specific binding spots showing a higher intensity signal, most spots exhibited background level intensity. (C) The coefficient of variation (CV) of 101,073 replicated probe pairs was observed to verify the binding consistency of Cbf1. Because higher intensity probes indicate more consistent binding properties, the consensus binding motif determined from the hierarchical rank order can be meaningful.