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Zhang P, Tao L, Zeng X, Qin C, Chen S, Zhu F, Li Z, Jiang Y, Chen W, Chen YZ. A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. Brief Bioinform 2017; 18:1057-1070. [PMID: 27542402 PMCID: PMC5862332 DOI: 10.1093/bib/bbw071] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Indexed: 02/06/2023] Open
Abstract
The genetic, proteomic, disease and pharmacological studies have generated rich data in protein interaction, disease regulation and drug activities useful for systems-level study of the biological, disease and drug therapeutic processes. These studies are facilitated by the established and the emerging computational methods. More recently, the network descriptors developed in other disciplines have become more increasingly used for studying the protein-protein, gene regulation, metabolic, disease networks. There is an inadequate coverage of these useful network features in the public web servers. We therefore introduced upto 313 literature-reported network descriptors in PROFEAT web server, for describing the topological, connectivity and complexity characteristics of undirected unweighted (uniform binding constants and molecular levels), undirected edge-weighted (varying binding constants), undirected node-weighted (varying molecular levels), undirected edge-node-weighted (varying binding constants and molecular levels) and directed unweighted (oriented process) networks. The usefulness of the PROFEAT computed network descriptors is illustrated by their literature-reported applications in studying the protein-protein, gene regulatory, gene co-expression, protein-drug and metabolic networks. PROFEAT is accessible free of charge at http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi.
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Affiliation(s)
- Peng Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
- College of Science, Sichuan Agricultural University, Yaan, P. R. China
| | - Lin Tao
- College of Science, Sichuan Agricultural University, Yaan, P. R. China
| | - Xian Zeng
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Chu Qin
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Shangying Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Feng Zhu
- College of Chemistry, Sichuan University, Chengdu, P. R. China
| | - Zerong Li
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, P. R. China
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab, Shenzhen Technology and Engineering Lab for Personalized Cancer Diagnostics and Therapeutics, and Shenzhen Kivita Innovative Drug Discovery Institute, Tsinghua University Shenzhen Graduate School, Shenzhen, P.R. China
| | - Weiping Chen
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Yu-Zong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
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