Nature exhibits modular design in biological systems. Gene module level analysis is based on this module concept, aiming to understand biological network design and systems behavior in disease and development by emphasizing on modules of genes rather than individual genes. Module level analysis has been extensively applied in genome wide level analysis, exploring the organization of biological systems from identifying modules to reconstructing module networks and analyzing module dynamics. Such module level perspective provides a high level representation of the regulatory scenario and design of biological systems, promising to revolutionize our view of systems biology, genetic engineering as well as disease mechanisms and molecular medicine.