A protein network refinement method based on module discovery and biological information

• Published in: BMC bioinformatics 2024-04, Vol.25 (1), p.157-157, Article 157
• Main Authors: Pan, Li, Wang, Haoyue, Yang, Bo, Li, Wenbin
• Format: Article
• Language: English
• Subjects: Accuracy; Algorithms; Analysis; Biological properties; Cell survival; Clustering; Computational biology; Computational Biology - methods; Gene expression; Graph theory; Health aspects; Identification; Identification of essential proteins; Information management; Localization; Methods; Modularity; Module discovery; Modules; Nodes; Performance enhancement; Performance evaluation; Protein Interaction Mapping - methods; Protein Interaction Maps; Protein-protein interactions; Proteins; Protein–protein interaction network; Ranking; Refined network; Research methodology; Researchers; RNA; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Therapeutic targets; Topology; Yeast
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05772-z

The identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover drug targets and prevent disease. Nowadays, node ranking methods are a common way to identify essential proteins, but the poor data quality of the underlying PIN has somewhat hindered the identification accuracy of essential proteins for these methods in the PIN. Therefore, researchers constructed refinement networks by considering certain biological properties of interacting protein pairs to improve the performance of node ranking methods in the PIN. Studies show that proteins in a complex are more likely to be essential than proteins not present in the complex. However, the modularity is usually ignored for the refinement methods of the PINs. Based on this, we proposed a network refinement method based on module discovery and biological information. The idea is, first, to extract the maximal connected subgraph in the PIN, and to divide it into different modules by using Fast-unfolding algorithm; then, to detect critical modules according to the orthologous information, subcellular localization information and topology information within each module; finally, to construct a more refined network (CM-PIN) by using the identified critical modules. To evaluate the effectiveness of the proposed method, we used 12 typical node ranking methods (LAC, DC, DMNC, NC, TP, LID, CC, BC, PR, LR, PeC, WDC) to compare the overall performance of the CM-PIN with those on the S-PIN, D-PIN and RD-PIN. The experimental results showed that the CM-PIN was optimal in terms of the identification number of essential proteins, precision-recall curve, Jackknifing method and other criteria, and can help to identify essential proteins more accurately.