Protein Complex Identification Based on Weighted PPI Network with Multi-Source Information

Publication date: Available online 11 June 2019Source: Journal of Theoretical BiologyAuthor(s): Yang Yu, Zeyu ZhengAbstractProteins form complexes to accomplish biological functions such as transcription of DNA, translation of mRNA and cell growth. Detection of protein complexes from protein-protein interaction (PPI) networks is the first step for the analysis of biological processes and pathways. Here, we propose a new framework by incorporating Gene Ontology (GO), amino acid background frequency (AABF) and data from von Mering (von Mering data) to identify protein complexes. Firstly, based on the semantic similarity of GO, we construct a weighted PPI network. Secondly, von Mering data is added to construct six types of weighted graphs. Lastly, by integrating density, diameter and cosine similarity, we define a new condition for clustering proteins in these weighted protein network by selecting specific node as ke node. Comparison and analysis results indicate that our proposed method could achieve better performances than some classic existing approaches in regard to f-measure and precision.

Source: Journal of Theoretical Biology - June 12, 2019 Category: Biology Source Type: research