Gastroenterology Department, Inner Mongolia People's Hospital, Hohhot, China.
Clinical Medical Research Center, Inner Mongolia People's Hospital, Hohhot, China.
J Comput Biol. 2020 Jun;27(6):965-974. doi: 10.1089/cmb.2019.0254. Epub 2019 Oct 9.
This study aimed to identify key functional modules and genes in functional module involved in hepatocellular carcinoma (HCC) development. The microarray data set GSE54236 was obtained from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between HCC, and normal samples were identified by Limma. DAVID was used to identify the gene ontology terms these genes enriched. The co-expression network was constructed based on Pearson correlation coefficient between gene expression values, and the functional modules these DEGs obviously enriched in were recognized through GraphWeb. Then, based on the genes related to the development of HCC, the DEGs interacting with HCC-associated genes were spotted. Finally, survival analysis and real-time quantitative polymerase chain reaction were performed. Totally, 427 upregulated (e.g., cell division cycle associated 5 [], kinesin family member 4A [], TPX2 microtubule nucleation factor []) and 313 downregulated (e.g., metallothionein 1E []) DEGs were identified in HCC. Besides, , , and had interacting relationship and played important roles in HCC development by interrelating with HCC-related gene, forkhead box M1 (). Furthermore, , , , and obviously enriched in cell cycle-related functional module, whereas enriched in mineral absorption module in Kyoto Encyclopedia of Genes and Genomes. , , and expression were increased in HCC cells, and their high expressions were related to poor prognosis. Overexpression of , , , and coregulated cell cycle and thereby promoted the development of HCC. The finding provided potential targets for the study and treatment of HCC.
本研究旨在鉴定与肝细胞癌(HCC)发展相关的功能模块中的关键功能模块和基因。从基因表达综合数据库(GEO)中获取微阵列数据集 GSE54236。通过 Limma 鉴定 HCC 和正常样本之间的差异表达基因(DEGs)。DAVID 用于识别这些基因富集的基因本体术语。根据基因表达值之间的 Pearson 相关系数构建共表达网络,并通过 GraphWeb 识别 DEGs 明显富集的功能模块。然后,基于与 HCC 发展相关的基因,鉴定与 HCC 相关基因相互作用的 DEGs。最后,进行生存分析和实时定量聚合酶链反应。总共鉴定出 427 个上调(例如细胞分裂周期相关蛋白 5[ ], 驱动蛋白家族成员 4A[ ], TPX2 微管成核因子[ ])和 313 个下调(例如金属硫蛋白 1E[ ])DEGs 在 HCC 中。此外,、、和具有相互作用关系,并通过与 HCC 相关基因叉头框 M1()相互作用,在 HCC 发展中发挥重要作用。此外,、、和明显富集于细胞周期相关功能模块,而在京都基因与基因组百科全书中富集于矿物质吸收模块。在 HCC 细胞中,、、和的表达增加,并且它们的高表达与不良预后相关。、、和的过表达共同调节细胞周期,从而促进 HCC 的发展。该研究结果为 HCC 的研究和治疗提供了潜在的靶点。