Active Protein Interaction Network and Its Application on Protein Complex Detection

In recent years, more and more attentions are focused on modelling and analyzing dynamic network. Some researchers attempted to extract dynamic network by combining the dynamic information from gene expression data or subcellular localization data with protein network. However, the dynamics of proteins' presence does not guarantee the dynamics of interactions, since the presence of a protein does not indicate the protein's activity. The activity of a protein is closely connected with its function. Thus only the dynamics of proteins activity ensure the dynamics of interaction. The gene expression of a cellular process or cycle carries more information than only the dynamics of proteins' presence. We assume that a protein is active when its expression values are near its maximum expression value, since the expression quantity will decrease after it has performed its function that leads a feedback for controlling the expression quantity. In this paper, we proposed a method to identify active time points for each protein in a cellular process or cycle by using a 3-sigma principle to compute an active threshold for each gene according to the characteristics of its expression curve. Combined the activity information and protein interaction network, we can construct an active protein interaction network (APPI). To demonstrate the efficiency of APPI network model, we applied it on complex detection. Compared with single threshold time series networks, APPI network achieves a better performance on protein complex prediction.