In-silico interaction-resolution pathway activity quantification and application to identifying cancer subtypes

BACKGROUND: Identifying subtypes of complex diseases such as cancer is the very first step toward developing highly customized therapeutics on such diseases, as their origins significantly vary even with similar physiological characteristics. There have been many studies to recognize subtypes of various cancer based on genomic signatures, and most of them rely on approaches based on the signatures or features developed from individual genes. However, the idea of network-driven activities of biological functions has gained a lot of interests, as more evidence is found that biological systems can show highly diverse activity patterns because genes can interact differentially across specific molecular contexts. METHODS: In this study, we proposed an in-silico method to quantify pathway activities with a resolution of genetic interactions for individual samples, and developed a method to compute the discrepancy between samples based on the quantified pathway activities. RESULTS: By using the proposed discrepancy measure between sample pathway activities in clustering melanoma gene expression data, we identified two potential subtypes of melanoma with distinguished pathway activities, where the two groups of patients showed significantly different survival patterns. We also investigated selected pathways with distinguished activity patterns between the two groups, and the result suggests hypotheses on the mechanisms driving the two potential subtypes. CONCLUSIONS: By using the proposed approach of modeling pathway activities with a resolution of genetic interactions, potential novel subtypes of disease were proposed with accompanying hypotheses on subtype-specific genetic interaction information.