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一个六基因支持向量机分类器有助于儿科感染性休克的诊断。

A six‑gene support vector machine classifier contributes to the diagnosis of pediatric septic shock.

机构信息

Department of The Intensive Care Unit, Eastern Hospital, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610101, P.R. China.

出版信息

Mol Med Rep. 2020 Mar;21(3):1561-1571. doi: 10.3892/mmr.2020.10959. Epub 2020 Jan 23.

DOI:10.3892/mmr.2020.10959
PMID:32016447
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7003034/
Abstract

Septic shock is induced by an uncontrolled inflammatory immune response to pathogens and the survival rate of patients with pediatric septic shock (PSS) is particularly low, with a mortality rate of 25‑50%. The present study explored the mechanisms of PSS using four microarray datasets (GSE26378, GSE26440, GSE13904 and GSE4607) that were obtained from the Gene Expression Omnibus database. Based on the MetaDE package, the consistently differentially expressed genes (DEGs) in the four datasets were screened. Using the WGCNA package, the disease‑associated modules and genes were identified. Subsequently, the optimal feature genes were further selected using the caret package. Finally, a support vector machine (SVM) classifier based on the optimal feature genes was built using the e1071 package. Initially, there were 2,699 consistent DEGs across the four datasets. From the 10 significantly stable modules across the datasets, four stable modules (including the magenta, purple, turquoise and yellow modules), in which the consistent DEGs were significantly enriched (P<0.05), were further screened. Subsequently, six optimal feature genes (including cysteine rich transmembrane module containing 1, S100 calcium binding protein A9, solute carrier family 2 member 14, stomatin, uridine phosphorylase 1 and utrophin) were selected from the genes in the four stable modules. Additionally, an effective SVM classifier was constructed based on the six optimal genes. The SVM classifier based on the six optimal genes has the potential to be applied for PSS diagnosis. This may improve the accuracy of early PSS diagnosis and suggest possible molecular targets for interventions.

摘要

脓毒性休克是由对病原体的失控性炎症免疫反应引起的,儿科脓毒性休克(PSS)患者的存活率特别低,死亡率为 25-50%。本研究使用从基因表达综合数据库(GEO)获得的四个微阵列数据集(GSE26378、GSE26440、GSE13904 和 GSE4607)来探讨 PSS 的机制。基于 MetaDE 包筛选了四个数据集的一致差异表达基因(DEGs)。使用 WGCNA 包鉴定与疾病相关的模块和基因。随后,使用 caret 包进一步选择最佳特征基因。最后,使用 e1071 包基于最优特征基因构建支持向量机(SVM)分类器。最初,四个数据集之间有 2699 个一致的 DEGs。从十个跨越数据集稳定的模块中,进一步筛选了四个稳定的模块(包括magenta、purple、turquoise 和 yellow 模块),其中一致的 DEGs 显著富集(P<0.05)。随后,从四个稳定模块中的基因中选择了六个最优特征基因(包括富含半胱氨酸的跨膜模块 1、S100 钙结合蛋白 A9、溶质载体家族 2 成员 14、stomatin、尿嘧啶磷酸化酶 1 和 utrophin)。此外,基于六个最优基因构建了有效的 SVM 分类器。基于六个最优基因的 SVM 分类器具有应用于 PSS 诊断的潜力。这可能会提高早期 PSS 诊断的准确性,并提示干预的可能分子靶点。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/3ff41d3accce/MMR-21-03-1561-g06.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/3ff41d3accce/MMR-21-03-1561-g06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/c56cc55f1db3/MMR-21-03-1561-g00.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/08674ee3e9e5/MMR-21-03-1561-g01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/653eedfd31e6/MMR-21-03-1561-g02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/26f26a1d7148/MMR-21-03-1561-g03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/0f23a989dc8d/MMR-21-03-1561-g04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/6b8a52d83f29/MMR-21-03-1561-g05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8d00/7003034/3ff41d3accce/MMR-21-03-1561-g06.jpg

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