Deciphering Transcription Factor Binding Patterns from Genome-Wide High Density ChIP-chip Tiling Array Data

The binding events of DNA-binding proteins can be extensively characterized by high density ChIP-chip tiling array data. The binding sites and binding occupancy patterns are all very useful to understand the DNA-protein interaction. We propose a statistical procedure which focuses on identifying the interaction signal regions and the patterns of interaction using peakedness and skewness tests. Its utility to annotate the binding signals by analyzing the Tbp1 and Rpb1 ChIP-chip datasets in fission yeast is demonstrated.