Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model

Figure 1

A simple example of the procedure of predicting lncRNA-protein interactions with LPIHN. (a) The lncRNA-lncRNA similarity matrix is calculated by using the expression profiles of lncRNAs to calculate the PCC of each pair of lncRNAs. The profile of known lncRNA-protein interactions is obtained where the value of and is 1 if there exists interaction between lncRNA and protein , otherwise 0. The PPI profile is obtained based on the normalized score of PPI. (b) The upper purple network is the lncRNA-lncRNA similarity network, the lower red network is the PPI network, and both of them are constructed based on the corresponding profile in (a). The heterogeneous network is constructed by connecting the lncRNA-lncRNA similarity network and PPI network together with the known lncRNA-protein interaction network. Purple triangles indicate lncRNAs, red circles proteins, purple edges lncRNA-lncRNA similarities, red edges protein-protein interactions, and black dotted edges known lncRNA-protein interactions. (c) Our method assigns a score to each of the candidate proteins of a query lncRNA, with the random walk with restart implemented on the heterogeneous network. The candidate proteins are ranked based on the score.