Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.