Many cancer predisposition and causative genes have been identified in the past few decades and have been extensively evaluated in primary tumors. The complex and highly heterogeneous nature of tumors requires more clinically useful candidate genes as prognostic, diagnostic, and therapeutic biomarkers for different subtypes of tumors and for predicting therapeutic response. Although genomics platforms have revealed the complex nature of tumors, integrative functional genomics approaches have the potential to provide a holistic understanding of the molecular genomic processes of carcinogenesis. While integration of the data gathered from genome and transcriptome is the simplest approach in integrative genomics, these approaches are also extended to analyze different levels of information, different cancer model systems, and multiple studies. Recent studies have revealed that integrative genomics has the potential to revolutionize the diagnosis and management of cancer by offering an unprecedented comprehensive understanding of cancer through unbiased experimental approaches. © 2010 MedUnion Press - http://www.mupnet.com.