Protein function annotation based on heterogeneous biological networks

• Published in: BMC bioinformatics 2022-11, Vol.23 (1), p.1-493, Article 493
• Main Authors: Hu, Sai, Luo, Yingchun, Zhang, Zhihong, Xiong, Huijun, Yan, Wei, Jiang, Meiping, Zhao, Bihai
• Format: Article
• Language: English
• Subjects: Algorithms; Annotations; Biological activity; Biological effects; Computer applications; Errors; Functionals; Gene expression; Heterogeneous biological network; Iterative methods; Methods; Multiplexing; Network propagation; Networks; Performance evaluation; Predictions; Propagation; Protein function prediction; Proteins; Statistical analysis; Topology
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-022-05057-3

Background Accurate annotation of protein function is the key to understanding life at the molecular level and has great implications for biomedicine and pharmaceuticals. The rapid developments of high-throughput technologies have generated huge amounts of protein–protein interaction (PPI) data, which prompts the emergence of computational methods to determine protein function. Plagued by errors and noises hidden in PPI data, these computational methods have undertaken to focus on the prediction of functions by integrating the topology of protein interaction networks and multi-source biological data. Despite effective improvement of these computational methods, it is still challenging to build a suitable network model for integrating multiplex biological data. Results In this paper, we constructed a heterogeneous biological network by initially integrating original protein interaction networks, protein-domain association data and protein complexes. To prove the effectiveness of the heterogeneous biological network, we applied the propagation algorithm on this network, and proposed a novel iterative model, named Propagate on Heterogeneous Biological Networks (PHN) to score and rank functions in descending order from all functional partners, Finally, we picked out top L of these predicted functions as candidates to annotate the target protein. Our comprehensive experimental results demonstrated that PHN outperformed seven other competing approaches using cross-validation. Experimental results indicated that PHN performs significantly better than competing methods and improves the Area Under the Receiver-Operating Curve (AUROC) in Biological Process (BP), Molecular Function (MF) and Cellular Components (CC) by no less than 33%, 15% and 28%, respectively. Conclusions We demonstrated that integrating multi-source data into a heterogeneous biological network can preserve the complex relationship among multiplex biological data and improve the prediction accuracy of protein function by getting rid of the constraints of errors in PPI networks effectively. PHN, our proposed method, is effective for protein function prediction.