Microarray assays and bioinformatics methods have identified many of the genes and associated regulatory DNAs that control the early phases of gastrulation in Drosophila. The localized activities of these genes are coordinated by a nuclear gradient of the maternal regulatory factor, Dorsal, that is established shortly after fertilization. At least half of the Dorsal target genes encode transcription factors or signaling components that lead to the restricted activation of FGF, EGF, and TGF-beta signaling pathways in the mesoderm, neurogenic ectoderm and dorsal ectoderm, respectively. Recent work has yielded insights into how these signaling pathways control gastrulation, particularly in the context of the Dorsal-mediated gene regulation network