Table_4_Identification of Key Modules and Hub Genes of Annulus Fibrosus in Intervertebral Disc Degeneration.XLSX

Background: Intervertebral disc degeneration impairs the quality of patients lives. Even though there has been development of many therapeutic strategies, most of them remain unsatisfactory due to the limited understanding of the mechanisms that underlie the intervertebral disc degeneration.
Questions/purposes: This study is meant to identify the key modules and hub genes related to the annulus fibrosus in intervertebral disc degeneration (IDD) through: (1) constructing a weighted gene co-expression network; (2) identifying key modules and hub genes; (3) verifying the relationships of key modules and hub genes with IDD; and (4) confirming the expression pattern of hub genes in clinical samples.
Methods: The Gene Expression Omnibus provided 24 sets of annulus fibrosus microarray data. Differentially expressed genes between the annulus fibrosus of degenerative and non-degenerative intervertebral disc samples have gone through the Gene Ontology (GO) and pathway analysis. The construction of a gene network and classification of genes into different modules were conducted through performing Weighted Gene Co-expression Network Analysis. The identification of modules and hub genes that were most related to intervertebral disc degeneration was proceeded. In order to verify the relationships of the module and hub genes with intervertebral disc degeneration, Ingenuity Pathway Analysis was operated. Clinical samples were adopted to help verify the hub gene expression profile.
Results: One thousand one hundred ninety differentially expressed genes were identified. Terms and pathways associated with intervertebral disc degeneration were presented by GO and pathway analysis. The construction of a Weighted Gene Coexpression Network was completed and clustering differentially expressed genes into four modules was also achieved. The module with the lowest P-value and the highest absolute correlation coefficient was selected and its relationship with intervertebral disc degeneration was confirmed by Ingenuity Pathway Analysis. The identification of hub genes and the confirmation of their expression profile were also realized.
Conclusions: This study generated a comprehensive overview of the gene networks underlying annulus fibrosus in intervertebral disc degeneration.
Clinical Relevance: Modules and hub genes identified in this study are highly associated with intervertebral disc degeneration, and may serve as potential therapeutic targets for intervertebral disc degeneration.

背景：椎间盘退变（intervertebral disc degeneration, IDD）会严重损害患者的生活质量。尽管目前已开发出多种治疗策略，但由于对椎间盘退变的潜在分子机制认知不足，多数治疗方案的疗效仍不尽如人意。
研究目的与问题：本研究旨在明确椎间盘退变患者纤维环（annulus fibrosus）相关的关键模块与核心基因，具体通过以下步骤实现：（1）构建加权基因共表达网络；（2）识别关键模块与核心基因；（3）验证关键模块及核心基因与椎间盘退变的关联；（4）明确核心基因在临床样本中的表达模式。
研究方法：本研究从基因表达综合数据库（Gene Expression Omnibus, GEO）获取了24组纤维环微阵列数据。对退变与非退变椎间盘样本的纤维环组织中的差异表达基因进行基因本体（Gene Ontology, GO）功能富集分析与通路富集分析。通过加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis）构建基因共表达网络，并将基因划分为不同模块，筛选与椎间盘退变相关性最强的模块及核心基因。为验证模块与核心基因与椎间盘退变的关联，采用Ingenuity通路分析（Ingenuity Pathway Analysis, IPA）进行验证，并借助临床样本验证核心基因的表达谱。
研究结果：本研究共筛选得到1190个差异表达基因。基因本体与通路富集分析揭示了与椎间盘退变相关的生物学过程与信号通路。成功构建加权基因共表达网络，并将差异表达基因聚类为4个模块。选取P值最低且绝对相关系数最高的模块，通过Ingenuity通路分析验证其与椎间盘退变的关联，同时完成核心基因的筛选及其表达谱的确认。
研究结论：本研究全面阐明了椎间盘退变患者纤维环组织的基因共表达网络调控特征。
临床意义：本研究筛选得到的关键模块与核心基因与椎间盘退变密切相关，可作为椎间盘退变潜在的治疗靶点。