Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models

Despite the considerable progress that has been made in cancer research, identifying cancer genes remains a significant challenge due to the intricate nature of the disease. Given the importance of incorporating gene interaction relationships in identifying potential cancer genes, Graph Neural Networks (GNNs) have garnered increasing attention for their ability to model gene associations effectively. Particularly, recent studies have demonstrated the superiority of GNNs in deciphering the knowledge embedded in Protein-Protein Interaction (PPI) networks for cancer gene prediction. However, these studies primarily focused on a single PPI network, overlooking the valuable insights encapsulated within other PPI networks. Additionally, previous endeavors often centered around pan-cancer datasets, neglecting the importance of predicting specific cancer genes. To address these limitations, we present a novel method called MPIT, which employs Graph Transformer Networks (GTNs) to identify specific cancer driver genes. MPIT effectively integrates data from diverse PPI and multi-omics data via the alignment and fusion of gene representations learned from different PPI networks. We collect three distinct cancer cell line datasets to assess the model performance. Our experimental findings demonstrate the superiority of MPIT over the existing methods, achieving the state-of-the-art performance across all three datasets.