Deep graph convolutional network-based multi-omics integration for cancer driver gene identification

Abstract Cancer driver genes play a pivotal role in understanding cancer development, progression, and therapeutic discovery. The plenty of accumulation of multi-omics data and biological networks provides a data foundation for graph neural network (GNN) frameworks. However, most existing methods directly concatenate multi-omics data as features, which may lead to limited performance. To address this limitation, we propose deepCDG, a deep graph convolutional network (GCN)-based multi-omics integration model for cancer driver gene identification. The model first employs shared-parameter GCN encoders to extract representations from three omics perspectives, followed by feature integration through an attention layer, and finally utilizes a residual-connected GCN predictor for cancer driver gene identification. Additionally, deepCDG employs GNNExplainer for cancer driver gene module identification. Experimental results demonstrate the effective predictive performance, model robustness, and computational efficiency of deepCDG. Additionally, biological interpretability analysis further validates the reliability of the identification of cancer driver genes of our framework, and the identified gene modules provide profound insights into complex inter-gene relationships and interactions. We believe our method offers enhanced applicability for cancer driver gene identification and could be extended to other biological research fields in future studies.