Until now, much of the focus in cancer has been on biomarker discovery and generating lists of univariately significant genes, as well as epidemiological and clinical measures. These approaches, although significant on their own, are not effective for elucidating the synergistic qualities of the numerous components in complex diseases. These components do not act one at a time, but rather in concert with numerous others. A compelling need exists to develop analytically sound and computationally advanced methods that elucidate a more biologically meaningful understanding of the mechanisms of cancer initiation and progression by taking these interactions into account.