The Gap Gene System of Drosophila melanogaster

The gap gene system of Drosophila melanogaster, part of the segmentation network, is one of the most well-studied developmental gene networks. It is an ideal system for benchmarking the performance of network inference algorithms because of the wealth and variety of data available and established knowledge of regulatory relationships controlling the system. We describe three recent efforts to fit wild-type spatiotemporal expression data, and to identify regulatory relationships between the genes de novo. These three efforts establish clear points of comparison regarding accuracy, correctness of regulatory architecture, and computational efficiency. We discuss the validation of these models against previous experimental work, and describe important directions for future research, including analysis of the less-well-understood pair-rule gene system and relating the promoter region composition with gene expression patterns and dynamics.