Assigning directionality to divergently transcribed promoters. For pairs of divergently transcribed genes sharing a single promoter region occupied by one or more transcription factors, our method can be used to determine which gene is regulated by which factor. In the diagrams, genes are represented as squares with arrows showing the transcription direction; transcription factors are shown as ovals. The numbers shown are significance scores for the coupling between the transcription factor and the gene, equal to the negative 10-based logarithm of the P-value. Significant regulatory relationships are shown as arrows to colored boxes. In (A), the cell cycle transcription factor Mbp1p regulates the recombinase RAD51 but not the endopeptidase PUP3, while in (B), the putative rRNA processing regulator Fhl1p regulates the ribosomal subunit RPL40B but not the protein kinase MLP1. In the scenario illustrated in (C), both Nrg1p and Hap6p bind to the intergenic upstream region of FSP2 and HXT9. The coupling analysis shows that Nrg1p in this case works bi-directionally and regulates both genes, while Hap6p regulates neither gene.