The study of gene regulatory networks is a particularly important research
area in Systems Biology. Although genome sequencing efforts have been tremendously
successful, much is unknown about the regulation of these sequenced genomes.
Computational and high-throughput experimental methods that decipher
regulatory mechanisms are crucial for understanding the regulatory network as a whole.
However, many new challenges are presented when studying gene regulation in a genome-wide context.
These challenges include:
- discovering cis-regulatory elements or DNA motifs in large genomes,
- making use of phylogenetic information from multiple genomes to study the evolution of regulatory mechanisms,
- the detection of weak regulatory signals through the integration of diverse types of genomic and binding data
such as chIP-chip, gene expression, protein localization and functional genomics,
- the detection of dynamic regulatory mechanisms due to changes in the cells environment
or progression through the cell cycle.
Novel methodology will be particularly relevant given the
hypothesis that the observed phenotypic differences between organisms with
very similar genomes may be due to variations in the gene regulation.