Identifying protein complexes from heterogeneous biological data

With the increasing availability of diverse biological information for proteins, integration of heterogeneous data becomes more useful for many problems in proteomics, such as annotating protein functions, predicting novel protein-protein interactions and so on. In this paper, we present an integrative approach called InteHC (Integrative Hierarchical Clustering) to identify protein complexes from multiple data sources. Although integrating multiple sources could effectively improve the coverage of current insufficient protein interactome (the false negative issue), it could also introduce potential false-positive interactions that could hurt the performance of protein complex prediction. Our proposed InteHC method can effectively address these issues to facilitate accurate protein complex prediction and it is summarized into the following three steps. First, for each individual source/feature, InteHC computes the matrices to store the affinity scores between a protein pair that indicate their propensity to interact or co-complex relationship. Second, InteHC computes a final score matrix, which is the weighted sum of affinity scores from individual sources. In particular, the weights indicating the reliability of individual sources are learned from a supervised model (i.e., a linear ranking SVM). Finally, a hierarchical clustering algorithm is performed on the final score matrix to generate clusters as predicted protein complexes. In our experiments, we compared the results collected by our hierarchical clustering on each individual feature with those predicted by InteHC on the combined matrix. We observed that integration of heterogeneous data significantly benefits the identification of protein complexes. Moreover, a comprehensive comparison demonstrates that InteHC performs much better than 14 state-of-the-art approaches. All the experimental data and results can be downloaded from http://www.ntu.edu.sg/home/zhengjie/data/InteHC.