Department of Orthopedics, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
Cell Cycle. 2020 Apr;19(8):884-894. doi: 10.1080/15384101.2020.1731054. Epub 2020 Mar 21.
This study aimed to identify co-expressed differentially expressed genes (DEGs) in quiescence and senescence of osteosarcoma (OS) U2OS cells and investigate their biological functions. GSE94805 from Gene Expression Omnibus database was extracted, involving 12 samples of OS U2OS cells (4 quiescence, 4 senescence, and 4 control samples). After analysis of DEGs by limma package, VENN analysis was performed to identify co-expressed DEGs in quiescence and senescent. The Cytoscape software was used to construct an interactive network of co-expressed DEGs. Finally, box-plot was drawn for the co-expressed DEGs in sub-network. Besides, the relation literatures were selected in GenCLiP database for the co-expressed DEGs. Seven hundred and forty-three DEGs (255 up-regulated genes, 488 down-regulated genes) were obtained in quiescence and 2135 DEGs (1189 up-regulated genes, 946 down-regulated genes) in senescence. Through VENN analysis, 448 DEGs (131 up-regulated genes, 317 down-regulated genes) were co-expressed in quiescent and senescence. In the co-expressed DEGs network, 896 nodes (448 nodes in quiescent, 448 nodes in senescent) were obtained. Finally, 16 co-expressed DEGs were obtained in the sub-network analysis, in which Aurora kinase A (AURKA) and polo-like kinase (PLK4) had been reported in OS. AURKA and PLK4 might be the key genes in quiescence and senescence of OS U2OS cells.
本研究旨在鉴定静息和衰老的骨肉瘤（OS）U2OS 细胞中共同表达的差异表达基因（DEGs），并研究其生物学功能。从基因表达综合数据库中提取 GSE94805，涉及 12 例 OS U2OS 细胞样本（4 例静息，4 例衰老，4 例对照样本）。使用 limma 包分析 DEGs 后，通过 VENN 分析鉴定静息和衰老中共同表达的 DEGs。使用 Cytoscape 软件构建共同表达 DEGs 的交互网络。最后，在子网络中绘制共同表达 DEGs 的箱线图。此外，在 GenCLiP 数据库中选择了相关文献，对共同表达的 DEGs 进行分析。在静息中获得了 743 个 DEGs（255 个上调基因，488 个下调基因），在衰老中获得了 2135 个 DEGs（1189 个上调基因，946 个下调基因）。通过 VENN 分析，在静息和衰老中共同表达了 448 个 DEGs（131 个上调基因，317 个下调基因）。在共同表达的 DEGs 网络中，获得了 896 个节点（静息中有 448 个节点，衰老中有 448 个节点）。最后，在子网络分析中获得了 16 个共同表达的 DEGs，其中 Aurora 激酶 A（AURKA）和 Polo 样激酶（PLK4）已在 OS 中报道。AURKA 和 PLK4 可能是 OS U2OS 细胞静息和衰老的关键基因。
