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Cancer arises from a stepwise accumulation of genetic changes through expansion of the malignant cell clones in the population of pre-malignant cells undergoing Darwinian selection process. In other words, cancer is an outcome of continuous and random acquisition of the changes in the genomes of individual cells. These modifications gradually and progressively change the phenotype of the normal cell making it more malignant through a loss of an overall stability of genome. The book summarizes bioinformatic methods to analyze the most general features of the malignant cell investigating molecular phenomena common for all tumor cells, with no regard to the characteristics related to tumor s tissue of origin. The results obtained in three independent modules of the book enhance a general understanding of cancer as an expression system comprising of the components dynamically interacting with each other. These results along with novel tools for in silico analysis of the cancer cell described in the book provide novel avenues for the functional genomics and systems biology of cancer and may be of help for large-scale computational modeling of cancer.