ReactomeFIFusion: Discovering Gene Fusion Events' Effects on Protein-Protein Interactions

Discovering the biological networks associated with pathogenetic mutations, such as gene fusion events, is an important step toward understanding the etiology and progression of cancer. The software pipeline presented in this work, ReactomeFIFusion, finds protein-protein interactions affected by cancer-associated gene fusion events. ReactomeFIFusion involves both integration of several existing databases and 3D structure modeling of protein-protein interactions. Using annotated protein-protein interactions from publicly available sources, including Interactome3D, INstruct, and PSISCORE, complexes simulated by the docking program ZDOCK, functional interactions provided by the Reactome Pathway Database, and fusion events annotated by the COSMIC database, ReactomeFIFusion reports normal pathways that may be affected by gene fusion events and the possible structural mechanisms based on protein 3D structures. Understanding the dysregulation of these pathways may help researchers to understand the possible causes of cancer and aid in guiding development of novel cancer treatments and therapies