Flowchart of our method and the examples of the outcomes. In the TF binding network, an oval represents a TF-encoding gene and a rectangle represents a gene whose gene product is not a TF. Examples of the three possible outcomes of our method for a given TF-gene pair are as follows. In Case 1a, HSP82 is a direct target of Hsf1. Hsf1 regulates HSP82 by directly binding to its promoter. In Case 1b, RPT4 is an indirect target of Hsf1. Hsf1 regulates RPT4 through the intermediate TF RPN4. In Case 2, YGR259C is regarded as a false positive in the original dataset because no path could be found from Hsf1 to YGR259C.
Yang and Wu BMC Systems Biology 2012 6:102 doi:10.1186/1752-0509-6-102