**6. Conclusions**

This chapter provides a summary of research into transcriptional regulatory networks controlling DNA repair pathways, bidirectional versus unidirectional promoters of DNA repair genes, and bidirectional promoters of breast and ovarian cancer genes. DNA words are shared among these promoters, and these words represent both known and unknown binding sites for transcription factors. When possible, we report the highest scoring assignment of transcription factor to DNA word. Our research represents a novel approach to identifying factors involved in transcriptional regulation of DNA repair genes. Many of these proteins have dual roles in transcription and DNA repair. Although many of the regulatory relationships are characterized at the level of protein-protein interactions, little research is available on the transcriptional regulatory networks that control DNA repair gene expression. We present evidence that regulatory networks exist among these genes, and support the claim that bidirectional promoters (implicated in B/O cancers) have a distinct network from unidirectional promoters. The identification of putative binding sites provides the first step in the elucidation of higher-order interdependencies among DNA repair genes in the cell. We also report preliminary findings on pairs of binding sites that represent regulatory modules. Furthermore, we show that there is much overlap among promoters of DNA repair genes, and that shared DNA binding motifs can be distributed among a collection of alternative promoters, each having distinct combinations of regulatory elements. The complex nature of the data can be simplified for visual interpretation using visualization techniques such as network modeling and circos diagrams.

Fig. 5. Relationships between genes and transcription factors.
