With the advancement of many high-throughput biotechnologies, an interest of many researchers has been to utilize multiple high-throughput data sources to gain further insights into biology and deeper understanding of complex diseases. In this talk, I will discuss briefly the different ways to interrogate multi-omics data and the different types of questions they addressed. Integration enable scientist to address and ask very specific question utilizing significant testing framework. More commonly, integration also enable us to explore and understand the complex relationships among different molecular phenotypes. I will discuss how rapidly emerging tools in networks research allow us to explore dynamic and static mutation-expression networks through coming exome sequencing and mRNA or protein data. Finally, the modeling of heterogeneity in multi-omics data together with extracting different types of features can help to improve the prognosis of disease outcome.