A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data

Essential proteins play an important role in various life activities and are considered to be a vital part of the organism. Gene expression data are an important dataset to construct dynamic protein-protein interaction networks (DPIN). The existing methods for the construction of DPINs generally utilize all features (or the features in a cycle) of the gene expression data. However, the features observed from successive time points tend to be highly correlated, and thus there are some redundant and irrelevant features in the gene expression data, which will influence the quality of the constructed network and the predictive performance of essential proteins. To address this problem, we propose a construction method of DPINs by using selected relevant features rather than continuous and periodic features. We adopt an improved unsupervised feature selection method based on Laplacian algorithm to remove irrelevant and redundant features from gene expression data, then integrate the chosen relevant features into the static protein-protein interaction network (SPIN) to construct a more concise and effective DPIN (FS-DPIN). To evaluate the effectiveness of the FS-DPIN, we apply 15 network-based centrality methods on the FS-DPIN and compare the results with those on the SPIN and the existing DPINs. Then the predictive performance of the 15 centrality methods is validated in terms of sensitivity, specificity, positive predictive value, negative predictive value, F-measure, accuracy, Jackknife and AUPRC. The experimental results show that the FS-DPIN is superior to the existing DPINs in the identification accuracy of essential proteins.