BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies.

Autor: Yang TH; Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, No. 1, University Road, Tainan City 701, Taiwan. Electronic address: thyangza@gs.ncku.edu.tw., Syu GD; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, No. 1, University Road, Tainan City 701, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan. Electronic address: guanda@gs.ncku.edu.tw., Chen CS; Department of Food Safety/Hygiene and Risk Management, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: cschen@gs.ncku.edu.tw., Chen GR; Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: asd02138787@gmail.com., Jhong SE; Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: kagura10856@gmail.com., Lin PH; Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: bb932156bb@gmail.com., Lin PC; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: peipei123.tw@gmail.com., Wang YC; Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: e14091091@gs.ncku.edu.tw., Shah P; Institute of Systems Biology and Bioinformatics, Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, No. 300, Zhongda Rd., Zhongli District, 320317 Taoyuan, Taiwan. Electronic address: prokonp@gmail.com., Tseng YY; Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA. Electronic address: ytseng@wayne.edu., Wu WS; Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan. Electronic address: wessonwu@mail.ncku.edu.tw.
Jazyk: angličtina
Zdroj: Computer methods and programs in biomedicine [Comput Methods Programs Biomed] 2024 Sep; Vol. 254, pp. 108260. Date of Electronic Publication: 2024 May 31.
DOI: 10.1016/j.cmpb.2024.108260
Abstrakt: Background and Objective: Proteome microarrays are one of the popular high-throughput screening methods for large-scale investigation of protein interactions in cells. These interactions can be measured on protein chips when coupled with fluorescence-labeled probes, helping indicate potential biomarkers or discover drugs. Several computational tools were developed to help analyze the protein chip results. However, existing tools fail to provide a user-friendly interface for biologists and present only one or two data analysis methods suitable for limited experimental designs, restricting the use cases.
Methods: In order to facilitate the biomarker examination using protein chips, we implemented a user-friendly and comprehensive web tool called BAPCP (Biomarker Analysis tool for Protein Chip Platforms) in this research to deal with diverse chip data distributions.
Results: BAPCP is well integrated with standard chip result files and includes 7 data normalization methods and 7 custom-designed quality control/differential analysis filters for biomarker extraction among experiment groups. Moreover, it can handle cost-efficient chip designs that repeat several blocks/samples within one single slide. Using experiments of the human coronavirus (HCoV) protein microarray and the E. coli proteome chip that helps study the immune response of Kawasaki disease as examples, we demonstrated that BAPCP can accelerate the time-consuming week-long manual biomarker identification process to merely 3 min.
Conclusions: The developed BAPCP tool provides substantial analysis support for protein interaction studies and conforms to the necessity of expanding computer usage and exchanging information in bioscience and medicine. The web service of BAPCP is available at https://cosbi.ee.ncku.edu.tw/BAPCP/.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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