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With advances in omics technologies, we now have the opportunity and challenge to gain more molecular insight not only at different omic levels respectively, but also from a holistic multi-omic perspective.Understanding physical and genetic interactions of molecules plays an essential role in the discovery of therapeutic targets and drug designs for complex diseases such as cancer.Different bioinformatics approaches have been proposed to help understand molecular interactions and to unravel different gene modules, regulatory pathways and networks at different levels.