网络回归嵌入揭示了基因调节的细胞类型转录因子协调
bioRxiv : the preprint server for biology
|November 14, 2023
概括
我们开发了NetREm,一个计算工具,以了解转录因子 (TF) 协调如何调节不同细胞类型的目标基因 (TG). 该方法确定了新的TF-TF协调链接及其在基因调节中的作用,并通过实验数据验证.
科学领域:
- 计算生物学是一种计算生物学.
- 基因组学就是基因组学.
- 系统生物学 系统生物学
背景情况:
- 转录因子 (TF) 协调对于通过蛋白质-蛋白质相互作用 (PPI) 和DNA联合结合的目标基因 (TG) 调节至关重要.
- 单细胞技术使基因表达分析成为可能,但不同细胞类型的TF协调和TG调节之间的联系仍然不清楚.
研究的目的:
- 开发一种新的计算方法,即网络回归嵌入 (NetREm),用于在TG监管中揭示特定细胞类型的TF-TF协调活动.
- 分析单细胞基因表达数据,通过利用网络受约束的规范化与先前的PPI知识.
主要方法:
- 在单细胞基因表达数据上开发了NetREm,这是一种使用网络受约束规范化的计算方法.
- 使用模拟数据和四个现实数据集 (mESC,hESC,HSC,mDC) 验证了NetREm.
- 应用NetREm对人类外周血液单核细胞 (PBMC),中枢和外周神经系统 (CNS/PNS) 细胞类型以及阿尔茨海默病 (AD) 模型.
主要成果:
- NetREm成功地确定了细胞类型协调TF和新的TF-TG候选链接.
- 使用Cut&Run,淘汰失效表达数据,eQTL和GWAS验证了顶级预测.
- 该研究揭示了特定于细胞类型的TF协调模式及其调节作用.
结论:
- NetREm是一个有效的工具,用于从单细胞数据中剖析细胞类型特定的TF协调和TG调节.
- 这些发现为各种细胞类型和疾病背景中的基因调节机制提供了新的见解.
- 这项工作有助于发现新的TF-TG相互作用及其遗传基础.
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