All cells in a multicellular organism contain the same genome, yet different cell types express different sets of genes. Recent advances in high throughput genomic technologies have opened up new opportunities to understand the gene regulatory network in diverse cell types in a genome-wide manner. Here, I discuss recent advances in experimental and computational approaches for the study of gene regulation in embryonic development from a systems perspective. This review is written for computational biologists who have an interest in studying developmental gene regulation through integrative analysis of gene expression, chromatin landscape, and signaling pathways. I highlight the utility of publicly available data and tools, as well as some common analysis approaches.