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PerturbDB用于解开基因功能和调控网络

Bing Yang¹, Man Zhang¹, Yanmei Shi¹

¹Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, Guangdong, 510120, China.

Nucleic acids research

|September 12, 2024

概括

PerturbDB是一个新的平台,可以轻松地重复使用 Perturb-Seq 数据用于基因功能发现. 它拥有66个数据集,有助于识别潜在的药物抑制剂和了解癌症中的基因作用.

科学领域:

基因组学就是基因组学.
系统生物学系统生物学
生物信息学是一种生物信息学.

背景情况:

Perturb-Seq是一种强大的方法,用于使用CRISPR和单细胞RNA测序进行高含量表型查.
由于缺乏可访问的数据再利用平台,现有的Perturb-Seq数据集未得到充分利用.

研究的目的:

开发 PerturbDB,这是一个用户友好的平台,用于访问和分析 Perturb-Seq 数据集.
为了促进基因功能发现,并了解基因调节作用在癌症等疾病.

主要方法:

整合了66个Perturb-Seq数据集 (4.5M+单细胞转录组),涵盖了19个细胞系的10,194个基因淘汰.
使用Mixscape算法统一处理数据.
基因按转录基因表型和综合化学扰动数据进行聚类.

主要成果:

根据乱的转录基因表型确定了421个基因群,其中157个在各种环境中稳定.
发现了1409个基因的552个潜在抑制剂,包括经过实验验证的mTOR抑制剂雷丁醇.
开发了一个"癌症"模块,用于研究癌症中的基因调节作用.

结论:

PerturbDB提供了使用 Perturb-Seq 数据进行基因功能研究的全面资源.
该平台增强了对复杂疾病,特别是癌症中的基因调节的理解.
PerturbDB的交互式界面可方便数据可视化,分析和下载,推动研究向前发展.

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