Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computatio

Background: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. Results: Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. Conclusion: We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The me...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Emmitt R. Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li
• Keywords: BMCBI 2005, Computational Genomic, Computational Genomic Analysis, Transcription Factor