A Special Structural Based Weighted Network Approach for the Analysis of Protein Complexes

Abstract

The detection and analysis of protein complexes is essential for understanding the functional mechanism and cellular integrity. Recently, several techniques for detecting and analysing protein complexes from Protein–Protein Interaction (PPI) dataset have been developed. Most of those techniques are inefficient in terms of detecting, overlapping complexes, exclusion of attachment protein in complex core, inability to detect inherent structures of underlying complexes, have high false-positive rates and an enrichment analysis. To address these limitations, we introduce a special structural-based weighted network approach for the analysis of protein complexes based on a Weighted Edge, Core-Attachment and Local Modularity structures (WECALM). Experimental results indicate that WECALM performs relatively better than existing algorithms in terms of accuracy, computational time, and p-value. A functional enrichment analysis also shows that WECALM is able to identify a large number of biologically significant protein complexes. Overall, WECALM outperforms other approaches by striking a better balance of accuracy and efficiency in the detection of protein complexes.

Keywords

• protein complexes
• core-attachment
• local modularity structure
• weighted PPI network