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Aljarallah NA, Dutta AK, Sait ARW. A Systematic Review of Genetics- and Molecular-Pathway-Based Machine Learning Models for Neurological Disorder Diagnosis. Int J Mol Sci 2024; 25:6422. [PMID: 38928128 DOI: 10.3390/ijms25126422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The process of identification and management of neurological disorder conditions faces challenges, prompting the investigation of novel methods in order to improve diagnostic accuracy. In this study, we conducted a systematic literature review to identify the significance of genetics- and molecular-pathway-based machine learning (ML) models in treating neurological disorder conditions. According to the study's objectives, search strategies were developed to extract the research studies using digital libraries. We followed rigorous study selection criteria. A total of 24 studies met the inclusion criteria and were included in the review. We classified the studies based on neurological disorders. The included studies highlighted multiple methodologies and exceptional results in treating neurological disorders. The study findings underscore the potential of the existing models, presenting personalized interventions based on the individual's conditions. The findings offer better-performing approaches that handle genetics and molecular data to generate effective outcomes. Moreover, we discuss the future research directions and challenges, emphasizing the demand for generalizing existing models in real-world clinical settings. This study contributes to advancing knowledge in the field of diagnosis and management of neurological disorders.
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Affiliation(s)
- Nasser Ali Aljarallah
- Department of Computer Science and Information Systems, College of Applied Sciences, AlMaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia
| | - Ashit Kumar Dutta
- Department of Computer Science and Information Systems, College of Applied Sciences, AlMaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia
| | - Abdul Rahaman Wahab Sait
- Department of Documents and Archive, Center of Documents and Administrative Communication, King Faisal University, Al-Ahsa, Al Hofuf 31982, Saudi Arabia
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Xiong T, Chen Y, Han S, Zhang TC, Pu L, Fan YX, Fan WC, Zhang YY, Li YX. Development and analysis of a comprehensive diagnostic model for aortic valve calcification using machine learning methods and artificial neural networks. Front Cardiovasc Med 2022; 9:913776. [PMID: 36531717 PMCID: PMC9751025 DOI: 10.3389/fcvm.2022.913776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Although advanced surgical and interventional treatments are available for advanced aortic valve calcification (AVC) with severe clinical symptoms, early diagnosis, and intervention is critical in order to reduce calcification progression and improve patient prognosis. The aim of this study was to develop therapeutic targets for improving outcomes for patients with AVC. MATERIALS AND METHODS We used the public expression profiles of individuals with AVC (GSE12644 and GSE51472) to identify potential diagnostic markers. First, the R software was used to identify differentially expressed genes (DEGs) and perform functional enrichment analysis. Next, we combined bioinformatics techniques with machine learning methodologies such as random forest algorithms and support vector machines to screen for and identify diagnostic markers of AVC. Subsequently, artificial neural networks were employed to filter and model the diagnostic characteristics for AVC incidence. The diagnostic values were determined using the receiver operating characteristic (ROC) curves. Furthermore, CIBERSORT immune infiltration analysis was used to determine the expression of different immune cells in the AVC. Finally, the CMap database was used to predict candidate small compounds as prospective AVC therapeutics. RESULTS A total of 78 strong DEGs were identified. The leukocyte migration and pid integrin 1 pathways were highly enriched for AVC-specific DEGs. CXCL16, GPM6A, BEX2, S100A9, and SCARA5 genes were all regarded diagnostic markers for AVC. The model was effectively constructed using a molecular diagnostic score system with significant diagnostic value (AUC = 0.987) and verified using the independent dataset GSE83453 (AUC = 0.986). Immune cell infiltration research revealed that B cell naive, B cell memory, plasma cells, NK cell activated, monocytes, and macrophage M0 may be involved in the development of AVC. Additionally, all diagnostic characteristics may have varying degrees of correlation with immune cells. The most promising small molecule medicines for reversing AVC gene expression are Doxazosin and Terfenadine. CONCLUSION It was identified that CXCL16, GPM6A, BEX2, S100A9, and SCARA5 are potentially beneficial for diagnosing and treating AVC. A diagnostic model was constructed based on a molecular prognostic score system using machine learning. The aforementioned immune cell infiltration may have a significant influence on the development and incidence of AVC.
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Affiliation(s)
- Tao Xiong
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yan Chen
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Shen Han
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Tian-Chen Zhang
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lei Pu
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yu-Xin Fan
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wei-Chen Fan
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ya-Yong Zhang
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ya-Xiong Li
- Department of Cardiovascular Surgery, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Yan’an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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