J Shanghai Jiaotong Univ Sci

Journal of Shanghai Jiaotong University(Science) >

2023 , Vol. 28 >Issue 4: 418

DOI: https://doi.org/10.1007/s12204-023-2584-0

Medicine-Engineering Interdisciplinary Research

Novel Scheme for Essential Proteins Identification Based on Improved Multicriteria Decision Making

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  • (1. School of Computer and Communication, Lanzhou University of Technology, Lanzhou 730050, China; 2. China Mobile Communications Group Gansu Co., Ltd., Lanzhou 730070, China)

Received date: 2021-08-17

  Accepted date: 2022-03-07

  Online published: 2023-07-31

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Abstract

Identifying essential proteins from protein-protein interaction networks is important for studies onbiological evolution and new drug’s development. Most of the presented criteria for prioritizing essential proteinsonly focus on a certain attribute of the proteins in the network, which suffer from information loss. In order toovercome this problem, a relatively comprehensive and effective novel method for essential proteins identificationbased on improved multicriteria decision making (MCDM), called essential proteins identification-technique fororder preference by similarity to ideal solution (EPI-TOPSIS), is proposed. First, considering different attributes ofproteins, we propose three methods from different aspects to evaluate the significance of the proteins: gene-degreecentrality (GDC) for gene expression sequence; subcellular-neighbor-degree centrality (SNDC) and subcellular-indegree centrality (SIDC) for subcellular location information and protein complexes. Then, betweenness centrality(BC) and these three methods are considered together as the multiple criteria of the decision-making model.Analytic hierarchy process is used to evaluate the weights of each criterion, and the essential proteins are prioritizedby an ideal solution of MCDM, i.e., TOPSIS. Experiments are conducted on YDIP, YMIPS, Krogan and BioGRIDnetworks. The results indicate that EPI-TOPSIS outperforms several state-of-the-art approaches for identifyingthe essential proteins through the performance measures.

Key words： protein-protein interaction network, essential proteins, multicriteria decision making (MCDM), biological information

Cite this article

LU Pengli1* (卢鹏丽)，CHEN Yuntian1 (陈云天)， LIAO Yonggang2 (廖永刚) . Novel Scheme for Essential Proteins Identification Based on Improved Multicriteria Decision Making[J]. Journal of Shanghai Jiaotong University(Science), 2023 , 28(4) : 418 . DOI: 10.1007/s12204-023-2584-0

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