Charting gene regulatory networks: strategies, challenges and perspectives

One of the foremost challenges in the post-genomic era will be to chart the gene regulatory networks of cells, including aspects such as genome annotation, identification of cis-regulatory elements and transcription factors, information on protein-DNA and protein-protein interactions, and data mining and integration. Some of these broad sets of data have already been assembled for building networks of gene regulation. Even though these datasets are still far from comprehensive, and the approach faces many important and difficult challenges, some strategies have begun to make connections between disparate regulatory events and to foster new hypotheses. In this article we review several different genomics and proteomics technologies, and present bioinformatics methods for exploring these data in order to make novel discoveries.