A network-guided penalized regression with application to proteomics data

Motivation Network theory has proven invaluable in unraveling complex protein interactions. Previous studies have employed statistical methods rooted in network theory, including the Gaussian graphical model, to infer networks among proteins, identifying hub proteins based on key structural properties of networks such as degree centrality. However, there has been limited research examining a prognostic role of hub proteins on outcomes, while adjusting for clinical covariates in the context of high-dimensional data. Results To address this gap, we propose a network-guided penalized regression method. First, we construct a network using the Gaussian graphical model to identify hub proteins. Next, we preserve these identified hub proteins along with clinically relevant factors, while applying adaptive Lasso to non-hub proteins for variable selection. Our network-guided estimators are shown to have variable selection consistency and asymptotic normality. Simulation results suggest that our method produces better results compared to existing methods and demonstrates promise for advancing biomarker identification in proteomics research. Lastly, we apply our method to the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data and identified hub proteins that may serve as prognostic biomarkers for various diseases, including rare genetic disorders and immune checkpoint for cancer immunotherapy. Availability and implementation R package is freely available on CRAN repository (https://CRAN.R-project.org/package=NetGreg) and published under General Public License version 3.