Identifying Potential miRNA Biomarkers for Gastric Cancer Diagnosis Using Machine Learning Variable Selection Approach

被引:13
|
作者
Gilani, Neda [1 ]
Arabi Belaghi, Reza [2 ,3 ]
Aftabi, Younes [4 ]
Faramarzi, Elnaz [5 ]
Edguenlue, Tuba [6 ]
Somi, Mohammad Hossein [5 ]
机构
[1] Tabriz Univ Med Sci, Fac Hlth, Dept Stat & Epidemiol, Tabriz, Iran
[2] Uppsala Univ, Dept Math, Uppsala, Sweden
[3] Univ Tabriz, Fac Math Sci, Dept Stat, Tabriz, Iran
[4] Tabriz Univ Med Sci, TB & Lung Dis Res Ctr, Tabriz, Iran
[5] Tabriz Univ Med Sci, Liver & Gastrointestinal Dis Res Ctr, Tabriz, Iran
[6] Mugla Sitki Kocman Univ, Fac Med, Dept Med Biol, Mugla, Turkey
关键词
miRNA; machine learning; boruta algorithm; gastric cancer; hsa-miR-1343-3p; AUC; GSE106817; GSE113486; MICRORNAS; ADENOCARCINOMA; PROGRESSION; CARCINOMA;
D O I
10.3389/fgene.2021.779455
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Aim: This study aimed to accurately identification of potential miRNAs for gastric cancer (GC) diagnosis at the early stages of the disease.Methods: We used GSE106817 data with 2,566 miRNAs to train the machine learning models. We used the Boruta machine learning variable selection approach to identify the strong miRNAs associated with GC in the training sample. We then validated the prediction models in the independent sample GSE113486 data. Finally, an ontological analysis was done on identified miRNAs to eliciting the relevant relationships.Results: Of those 2,874 patients in the training the model, there were 115 (4%) patients with GC. Boruta identified 30 miRNAs as potential biomarkers for GC diagnosis and hsa-miR-1343-3p was at the highest ranking. All of the machine learning algorithms showed that using hsa-miR-1343-3p as a biomarker, GC can be predicted with very high precision (AUC; 100%, sensitivity; 100%, specificity; 100% ROC; 100%, Kappa; 100) using with the cut-off point of 8.2 for hsa-miR-1343-3p. Also, ontological analysis of 30 identified miRNAs approved their strong relationship with cancer associated genes and molecular events.Conclusion: The hsa-miR-1343-3p could be introduced as a valuable target for studies on the GC diagnosis using reliable biomarkers.
引用
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页数:10
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