2022 • In BHI-BSN 2022 - IEEE-EMBS International Conference on Biomedical and Health Informatics and IEEE-EMBS International Conference on Wearable and Implantable Body Sensor Networks, Symposium Proceedings
Mass Spectrometry; Proteomics; SomaScan; Systemic Autoinflammatory Diseases; Conventional machines; Disease classification; False discovery rate; Machine learning algorithms; Predictive capabilities; Proteomic approaches; Separate analysis; Somascan; Systemic autoinflammatory disease; Artificial Intelligence; Computer Science Applications; Information Systems; Information Systems and Management; Biomedical Engineering; Instrumentation
Abstract :
[en] A cross-analysis study was conducted to compare proteomic platforms in classifying patients with Systemic Autoinflammatory diseases, using proteins extracted from different profiling experiments. The datasets used were obtained from SomaScan assays and Mass Spectrometry (MS). A separate analysis was performed to each dataset based on the false discovery rate (FDR) in order to extract statistically important proteins. Conventional machine learning algorithms were subsequently employed to evaluate the denoted proteins as candidate biomarkers and compare the predictive capabilities of the two proteomic platforms. Using the SomaScan assay, we managed to achieve higher classification metrics compared to the MS dataset. An improvement was also attained on the classification results when the features used were extracted from the MS data and applied on the SomaScan dataset, compared to the opposite combination. Finally, the proteins derived from the FDR analysis in both datasets proved to be highly correlated regarding their importance score.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Papagiannopoulos, Orestis D.; University of Ioannina, Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, Ioannina, Greece
Papaloukas, Costas; Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology (FORTH-IMBB), Dept. of Biological Applications and Technology, University of Ioannina, Dept. of Biomedical Research, Ioannina, Greece
Pezoulas, Vasileios C.; University of Ioannina, Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, Ioannina, Greece
Van De Werken, Harmen J.G.; Erasmus MC Cancer Institute, University Medical Center, Dept. of Immunology, Rotterdam, Netherlands
Poulet, Christophe ; Centre Hospitalier Universitaire de Liège - CHU > > Service de rhumatologie ; Laboratory of Rheumatology, GIGA-Research CHULiege, Liege, Belgium
Mueller, Yvonne M.; Erasmus MC Cancer Institute, University Medical Center, Dept. of Immunology, Rotterdam, Netherlands
Katsikis, Peter D.; Erasmus MC Cancer Institute, University Medical Center, Dept. of Immunology, Rotterdam, Netherlands
de Seny, Dominique ; Centre Hospitalier Universitaire de Liège - CHU > > Service de rhumatologie ; Erasmus MC Cancer Institute, University Medical Center, Dept. of Immunology, Rotterdam, Netherlands
Fotiadis, Dimitrios I.; Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology (FORTH-IMBB), Dept. of Biological Applications and Technology, University of Ioannina, Dept. of Biomedical Research, Ioannina, Greece
Language :
English
Title :
Comparison of Proteomic Approaches in Autoinflammatory Disease Classification
Publication date :
2022
Event name :
2022 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)
Event place :
Ioannina, Grc
Event date :
27-09-2022
Audience :
International
Main work title :
BHI-BSN 2022 - IEEE-EMBS International Conference on Biomedical and Health Informatics and IEEE-EMBS International Conference on Wearable and Implantable Body Sensor Networks, Symposium Proceedings
Publisher :
Institute of Electrical and Electronics Engineers Inc.
IEEE IEEE Engineering in Medicine and Biology Society (EMBS) IEEE Open Journal of Engineering in Medicine and Biology (OJEMB) Medical Technology and Intelligent Information Systems (MEDLAB) Rizarios Foundation
Funding text :
This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 779295 (ImmunAID – Immunome project consortium for AutoInflammatory Disorders).This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 779295 (ImmunAID - Immunome project consortium for AutoInflammatory Disorders).
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.
Bibliography
P. Efthimiou, P. Paik, L. Bielory, "Diagnosis and management of adult onset Still's disease" , Annals of the rheumatic diseases, 65.5, pp. 564-572, 2006.
A. Betrains et al., "Systemic autoinflammatory disease in adults", Autoimmunity Reviews 20.4, 2021.
G. Donato et al., "Monogenic Autoinflammatory Diseases: State of the Art and Future Perspectives", International Journal of Molecular Sciences 22.12, 2021.
J. Krainer, S. Siebenhandl, A. Weinhäusel, "Systemic autoinflammatory diseases", Journal of autoimmunity 109, 102421, 2020.
R. Liu et al., "Comparison of proteomic methods in evaluating biomarker-AKI associations in cardiac surgery patients", Translational Research 238, pp. 49-62, 2021.
M. Dunn, R. Jimenez, J. Chaput, "Analysis of aptamer discovery and technology", Nature Reviews Chemistry 1.10, pp. 1-16, 2017.
T. Fong et al., "Identification of plasma proteome signatures associated with surgery using SOMAscan", Annals of surgery 273.4, 732, 2021.
E. Begic et al., "SOMAscan-based proteomic measurements of plasma brain natriuretic peptide are decreased in mild cognitive impairment and in Alzheimer's dementia patients", PloS one 14.2, 2019.
O. Govaere et al., "Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis", Science translational medicine 12.572, 2020.
Y. Luo et al., "SOMAscan proteomics identifies serum biomarkers associated with liver fibrosis in patients with NASH", Hepatology Communications 5.5, pp. 760-773, 2021.
G. Chen et al., "Serum proteome analysis of systemic JIA and related lung disease identifies distinct inflammatory programs and biomarkers", Arthritis & Rheumatology, 2022.
L. Zhang et al., "Differential protein analysis of serum exosomes post-intravenous immunoglobulin therapy in patients with Kawasaki disease", Cardiology in the Young 27.9, pp. 1786-1796, 2017.
Y. Zhou et al., "Identification of a novel anti-heat shock cognate 71 kDa protein antibody in patients with Kawasaki disease", Molecular medicine reports 21.4, pp. 1771-1778, 2020.
A. Kirectepe et al., "Peripheral blood mononuclear cell proteome profile in Behçet's syndrome", Rheumatology International 40.1, pp. 65-74, 2020.
W. Zheng et al., "Metabolomic alterations associated with Behçet's disease", Arthritis research & therapy 20.1, pp. 1-10 2018.
J. Cox et al., "Andromeda: a peptide search engine integrated into the MaxQuant environment", Journal of proteome research 10.4, pp. 1794-1805, 2011.
F. Pedregosa et al., "Scikit-learn: Machine learning in Python" , the Journal of machine Learning research 12, pp. 2825-2830, 2011.
Y. Benjamini, Y. Hochberg, "Controlling the false discovery rate: a practical and powerful approach to multiple testing" , Journal of the Royal statistical society: series B (Methodological), 57.1, pp. 289-300, 1995.
D. Freedman, R Pisani, R Purves, "Statistics" . Pisani, R Purves, 4th edn. WW Norton & Company, New York, 2007.
T. Edgar, D. Manz, "Research methods for cyber security" , Syngress, 2017.
G. Brown et al., "Gene: a gene-centered information resource at NCBI", Nucleic acids research 43, D36-D42, 2015.
M. Altiparmak et al., "Colchicine neuromyopathy: a report of six cases", Clinical and experimental rheumatology 20.4, 2002.
Y. Yamanishi et al., "A case of cyclosporin A-induced myopathy", Ryumachi.[Rheumatism] 33.1, pp. 63-67, 1993.
B. Guezguez et al., "Dual role of melanoma cell adhesion molecule (MCAM)/CD146 in lymphocyte endothelium interaction: MCAM/CD146 promotes rolling via microvilli induction in lymphocyte and is an endothelial adhesion receptor", The Journal of Immunology 179.10, pp. 6673-6685, 2007.
Similar publications
Sorry the service is unavailable at the moment. Please try again later.
This website uses cookies to improve user experience. Read more
Save & Close
Accept all
Decline all
Show detailsHide details
Cookie declaration
About cookies
Strictly necessary
Performance
Strictly necessary cookies allow core website functionality such as user login and account management. The website cannot be used properly without strictly necessary cookies.
This cookie is used by Cookie-Script.com service to remember visitor cookie consent preferences. It is necessary for Cookie-Script.com cookie banner to work properly.
Performance cookies are used to see how visitors use the website, eg. analytics cookies. Those cookies cannot be used to directly identify a certain visitor.
Used to store the attribution information, the referrer initially used to visit the website
Cookies are small text files that are placed on your computer by websites that you visit. Websites use cookies to help users navigate efficiently and perform certain functions. Cookies that are required for the website to operate properly are allowed to be set without your permission. All other cookies need to be approved before they can be set in the browser.
You can change your consent to cookie usage at any time on our Privacy Policy page.
