Figure 1.

Overview of the method. (a) Splitting the genome-wide location (ChIP-chip) data into several coexpressed gene sets. Each of the derived target gene sets was called an IMC. Each IMC was named after the transcription factor of the ChIP-chip data followed by a serial number. Gray rectangles indicate the IMCs. Small dots indicate the genes bound to the transcription factor. (b) Generation of preEPMs. The IMCs with similar mean expression patterns were grouped for further analysis. (c) Detecting the regulators in each IMC. Initially, the over-represented motifs in each IMC were detected by the t-test. Next, biologically significant motif evidence and ChIP-chip evidence were selected using a test based on the hypergeometric distribution. Subsequently, in the case of motif evidence, recurrently confirmed motifs in each preEPM were selected. Yellow diamonds and ellipses indicate biologically significant regulators. Gray diamonds and ellipses represent the regulators that were not qualified by the test. Gray curved lines between the regulators indicate synergistic pairs. (d) Identification of an EPM. For each preEPM, the IMCs without a confirmed regulator were eliminated, and the retained IMCs and their corresponding regulators were arranged. Solid lines indicate motif evidence, and dotted lines indicate ChIP-chip evidence. (e) Identification of an RM. Regulators with highly overlapped target genes were united to identify an RM.