Construction of Gene Regulatory Networks

A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. Constructing the GRNs of an organism can increase our understanding of the organization and processes of gene regulation in the organism. To do this, however, one needs to have a large number of TF binding sites (TFBSs), which are required for predicting the target genes of TFs. The identification of TFBSs used to be a highly challenging task, but recent advances have made it much simpler. However, computational predictions of TFBSs are still much needed because even in Arabidopsis less than 50% of the TFs have known TFBSs. The next challenge is how to predict the target genes of a given TF. But the most challenging part is how to identify the upstream regulators of a gene of interest. In my talk, I shall present a method for predicting the TFBS of a TF, a method for predicting the target genes of a TF and a method for predicting the upstream regulators of a gene.