Complex Networks, Gene Expression and Cancer Complexity: A Brief Review of Methodology and Applications

In this brief survey, various aspects of cancer complexity and how this complexity can be confronted using modern complex networks’ theory and gene expression datasets, are described. In particular, the causes and the basic features of cancer complexity, as well as the challenges it brought are underlined, while the importance of gene expression data in cancer research and in reverse engineering of gene co-expression networks is highlighted. In addition, an introduction to the corresponding theoretical and mathematical framework of graph theory and complex networks is provided. The basics of network reconstruction along with the limitations of gene network inference, the enrichment and survival analysis, evolution, robustness-resilience and cascades in complex networks, are described. Finally, an indicative and suggestive example of a cancer gene co-expression network inference and analysis is given.