Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model.
Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model.
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DOI：
10.1016/j.heliyon.2022.e11905
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发表时间：
2022-11
期刊：
影响因子：
4
通讯作者：
Pan, Silin
中科院分区：
文献类型：
--
作者：
Sun, Hongxiao;Liu, Changying;Zhang, Xu;Liu, Panpan;Du, Zhanhui;Luo, Gang;Pan, Silin
关键词：
通过生物信息学分析，发现了川崎病（KD）异常甲基化差异表达基因（MDEG），并建立了KD的随机森林诊断模型。从Gene Expression Omnibus（GEO）检索并下载表达（GSE 18606、GSE 68004、GSE 73461）和甲基化（GSE 109430）图谱。我们使用R软件进行富集分析。此外，我们构建了一个蛋白质相互作用网络，并获得了6个枢纽基因。我们使用来自GEO的表达谱GSE 100154来验证枢纽基因。最后，我们构建了一个基于随机森林的诊断模型。我们共获得55个MDEG（43个高甲基化，低表达基因和12个低甲基化，高表达基因）。通过Cytoscape软件鉴定了6个枢纽基因（CD 2、IL 2 RB、IL 7 R、CD 177、IL 1 RN和MYL 9）。六个枢纽基因的曲线下面积（AUC）为0.745至0.898，并且组合的AUC为0.967。随机森林诊断模型显示AUC为0.901。6个新的中枢基因的发现，加深了对KD发病机制的认识，所建立的模型可用于KD的准确诊断，为临床诊断提供依据。差异表达基因;综合基因表达;川崎;蛋白质相互作用网络;随机森林。
By using bioinformatics analysis, abnormal methylated differentially expressed genes (MDEGs) in Kawasaki disease (KD) were identified and a random forest diagnostic model for KD was established. The expression (GSE18606, GSE68004, GSE73461) and methylation (GSE109430) profiles was retrieved and download from Gene Expression Omnibus (GEO). We conducted enrichment analyses by using R software. In addition, we constructed a protein interaction network, and obtained 6 hub genes. We used expression profiles GSE100154 from GEO to verify the hub genes. Finally, we constructed a diagnostic model based on random forest. We got a total of 55 MDEGs (43 hyper-methylated, low-expressing genes and 12 hypo-methylated, high-expressed genes). Six hub genes (CD2, IL2RB, IL7R, CD177, IL1RN, and MYL9) were identified by Cytoscape software. The area under curve (AUC) of the six hub genes was from 0.745 to 0.898, and the combined AUC was 0.967. The random forest diagnostic model showed that AUC was 0.901. The identification of 6 new hub genes improves our understanding of the molecular mechanism of KD, and the established model can be employed for accurate diagnosis and provide evidence for clinical diagnosis. Differentially expressed genes; Gene expression omnibus; Kawasaki disease; Protein-protein interactioNn etwork; Random forest.
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影响因子：
2.5
作者：
Huang, Ying-Hsien;Lo, Mao-Hung;Kuo, Ho-Chang
通讯作者：
Kuo, Ho-Chang
影响因子：
5.1
作者：
Furuno, K;Yuge, T;Hara, T
通讯作者：
Hara, T
影响因子：
16.6
作者：
Altman MC;Rinchai D;Baldwin N;Toufiq M;Whalen E;Garand M;Syed Ahamed Kabeer B;Alfaki M;Presnell SR;Khaenam P;Ayllón-Benítez A;Mougin F;Thébault P;Chiche L;Jourde-Chiche N;Phillips JT;Klintmalm G;O'Garra A;Berry M;Bloom C;Wilkinson RJ;Graham CM;Lipman M;Lertmemongkolchai G;Bedognetti D;Thiebaut R;Kheradmand F;Mejias A;Ramilo O;Palucka K;Pascual V;Banchereau J;Chaussabel D
通讯作者：
Chaussabel D
影响因子：
21.3
作者：
通讯作者：
--
影响因子：
5.2
作者：
FURUKAWA, S;MATSUBARA, T;YABUTA, K
通讯作者：
YABUTA, K