Maturing low-cost acquisition technology of multi-omics data, e.g. transcriptome and proteome data, continues to generate extensive amounts of cellular response data in numerous physiological and pathological condition. Researchers can use these data to explore the mechanism of biological processes, infer the generation and development of diseases, and discover the targets of drugs. In 2010, the National Institutes of Health (NIH) launched a project named Library of Integrated Network-based Cellular Signatures (LINCS). The project established an integrated network-based cellular response database by measuring the change of gene expression and other levels of cellular response after a series of perturbations, illustrated that how cell reacts under multiple genetic and environmental stresses, and connected basic medical research and clinical therapy to promote the rapid development of translational medicine. Here we review the origin, significance, experimental technology, quality control, data content and analysis tools of the LINCS project. We also summarize the applied research of the LINCS project in the aspects of gene regulation, disease generation, and adverse drug reactions.