Trans-omics analysis of the difference between Cortical and Trabecular bone.

皮质骨和小梁骨之间差异的跨组学分析。

• 批准号: 21K09998
• 负责人: Rosales Marcelo
• 金额: $ 2.66万
• 依托单位: Niigata University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2021
• 资助国家: 日本
• 起止时间: 2021-04-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-21K09998/
• 关键词: trans-omics; extracellular matrix; bone phenotype; bone regeneration

In this study, a bioinformatic methodology employing trans-omics analysis and the Matrisome database is being employed to investigate the differences in extracellular matrix composition and the associated regulatory networks between cortical and trabecular bone.During this period, FASTQ files analysis workflow was stablished and Gene Read Counts trials were performed. RNA sequencing environment for Weighted gene co-expression network analysis setting was completed to identify modules or groups of genes that exhibit similar expression patterns across different samples. This method assigns weights to gene-gene connections based on the strength of their co-expression relationships, allowing the identification of highly interconnected gene modules and the functional relationships and regulatory mechanisms underlying biological processes by identifying key genes within modules and elucidating their potential roles in specific biological pathways or diseases.DESeq2/Limma for fold change and gene list environment was set for Pathway analysis to perform enrichment analysis and visualize the results, to gain insights into the bone biological systems and to identify potential targets for therapeutic intervention.

本研究采用生物信息学的方法，结合trans-omics分析和Matrisome数据库，研究了皮质骨和松质骨细胞外基质组成和相关调控网络的差异，建立了FASTQ文件分析流程，并进行了基因读数试验。完成用于加权基因共表达网络分析设置的RNA测序环境，以鉴定在不同样品中表现出相似表达模式的基因模块或基因组。该方法基于基因-基因连接的共表达关系的强度为基因-基因连接分配权重，通过识别模块内的关键基因并阐明其在特定生物学途径或疾病中的潜在作用，允许识别高度互连的基因模块以及生物学过程的功能关系和调控机制。为Pathway分析设置了倍数变化和基因列表环境的Limma，以进行富集分析并可视化结果，从而深入了解骨生物学系统并鉴定治疗干预的潜在靶标。