Both average-level and probe-level analyses were performed. In the average-level analysis, we focused on the regulatory regions near the transcription start sites (from 1,300-bp upstream and 500bp downstream of the transcription start sites). This approach avoided noise caused by distal oligonucleotides residing in the upstream intergenic regions and provided a more focused analysis of the region where most transcription factors bind, while allowing our results to be compared with other studies focused on human promoters (Weber et al., 2007).
