Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
Clin Rheumatol. 2021 Sep;40(9):3745-3754. doi: 10.1007/s10067-021-05649-z. Epub 2021 Mar 6.
This study aimed to identify osteoarthritis (OA) related genes based on microarray data in synovium with a more robust integrative analysis method.
Four series GSE55457, GSE12021, GSE55235, and GSE55584 (36 OA and 29 normal samples) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) of GSE55457, GSE12021, and GSE55235 were identified using the LIMMA package. Overlapping DEGs from the intersection of the three series were detected. Simultaneously, samples in the four series were pooled to identify DEGs with integrated analysis using the Sva package.
In total, 74 overlapping DEGs and 242 DEGs by integrating four series were detected. Based on them, 70 common DEGs were used to construct a protein-protein interaction (PPI) network, involving 61 nodes and 206 edges. Also, three gene modules and five hub genes, named JUN, IL6, VEGFA, MYC, and EGR1, were identified.
Seventy DEGs were finally identified with a more robust integrative analysis method. JUN, IL6, VEGFA, MYC, and EGR1 were identified as hub genes in the development of OA. Key Points • 76 overlapping DEGs were detected from the intersection of DEGs in GSE55457, GSE12021, and GSE55235. • 242 DEGs were identified by integrating four series using Sva package. • 72 common DEGs were finally identified based on the overlapping DEGs and the integrated DEGs. • JUN, IL6, VEGFA, MYC, and EGR1 were identified as hub genes in the development of OA.
本研究旨在基于滑膜的微阵列数据，采用更稳健的综合分析方法，鉴定骨关节炎（OA）相关基因。
从基因表达综合数据库中下载了四个系列的 GSE55457、GSE12021、GSE55235 和 GSE55584（36 个 OA 样本和 29 个正常样本）。使用 LIMMA 包鉴定 GSE55457、GSE12021 和 GSE55235 中的差异表达基因（DEGs）。通过三个系列的交集检测重叠的 DEGs。同时，使用 Sva 包对四个系列的样本进行综合分析，以鉴定 DEGs。
共检测到 74 个重叠 DEGs 和 242 个综合四个系列的 DEGs。在此基础上，构建了一个包含 61 个节点和 206 个边的蛋白-蛋白相互作用（PPI）网络，涉及 70 个共同的 DEGs。还鉴定了三个基因模块和五个枢纽基因，分别命名为 JUN、IL6、VEGFA、MYC 和 EGR1。
采用更稳健的综合分析方法最终确定了 70 个 DEGs。JUN、IL6、VEGFA、MYC 和 EGR1 被鉴定为 OA 发生发展的枢纽基因。
在 GSE55457、GSE12021 和 GSE55235 的 DEGs 交集处检测到 76 个重叠 DEGs。
使用 Sva 包整合四个系列，鉴定到 242 个 DEGs。
基于重叠 DEGs 和整合 DEGs，最终确定了 72 个共同的 DEGs。
JUN、IL6、VEGFA、MYC 和 EGR1 被鉴定为 OA 发生发展的枢纽基因。
