Cancer research has rapidly incorporated high throughput technologies into its research, using various microarray, tissue array, and next generation sequencing platforms. The result has been a rapid increase in cancer data output and data types. Now more than ever, having the informatic skills and knowledge of available bioinformatic resources specific to cancer is critical. Although data management and integration are important, data analysis and interpretation are the rate-limiting steps for achieving biological understanding and therapeutic progress. Effective integration of scientific bioinformatics into biology is essential for the future of cancer therapeutics. As a case study of data integration and the use of different bioinformatics tools we present our experience in the identification of the molecular target and the mechanism of action of the CIGB-552 peptide. Differential gene expression studies identified the pathways and biological processes modulated by CIGB-552. On the other hand, proteomics studies revealed that CIGB-552 interacts with biological complexes essential for the proliferation and survival of tumor cells. These findings provide elements on the molecular bases that contribute to justify the cytotoxic mechanism of CIGB-552. While the application of bioinformatics to cancer research has allowed for astounding progress, significant challenges remain. The challenges associated with the selection of different analysis techniques, pipelines, databases will be discussed.