DualMarker: A Multi-Source Fusion Identification Method for Prognostic Biomarkers of Breast Cancer Based on Dual-Layer Heterogeneous Network

Breast cancer is a complex disease that arises from multiple factors, including genetics, age, and environmental factors. Prognosis prediction for breast cancer is a challenging task that urgently needs to be addressed. Prognostic biomarkers can aid in predicting clinical outcomes for breast cancer patients, and network-based approaches are frequently employed to identify such biomarkers. However, the accuracy of these approaches based on single source biological network is poor due to incomplete interactions of single biological network. Some network-based approaches that integrate multiple biological networks have not considered network denoising, which may lead to the accuracy of these approaches to be improved. We propose a multi-source fusion identification method named DualMarker for prognostic biomarkers of breast cancer. This method constructs a dual-layer heterogeneous network by integrating multiple biological sources. To decrease the negative effects of incomplete interactions in biological networks, we denoise the constructed network. The ranking of features is obtained by the network propagation algorithm and the initial scoring strategy. Compared with six other network-based methods, DualMarker shows the best performance in six breast cancer datasets. Moreover, we have also demonstrated that the biomarkers identified by DualMarker are of interpretability biologically and closely associated with breast cancer patients’ prognosis.