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LnCeCell 2.0:基于单细胞和空间转录组学测序数据的 lncRNA 相关 ceRNA 网络和网络工具的更新资源
Qiuyan Guo1, Qian Liu2, Danni He2
1Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China.
Nucleic acids research
|October 29, 2024
概括
LnCeCell 2.0 是长非编码RNA (lncRNA) 相关的竞争性内源RNA (ceRNA) 网络的更新数据库,提供单细胞和空间转录组学的见解. 本资源有助于理解各种生物环境中的复杂调节机制.
科学领域:
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
- 分子生物学分子生物学
背景情况:
- 长非编码RNAs (lncRNAs) 通过竞争的内源RNA (ceRNA) 网络在基因调节中发挥关键作用.
- 了解单细胞和空间分辨率的ceRNA相互作用对于破译复杂的生物过程和疾病至关重要.
- 现有的资源往往缺乏全面的数据集成和单细胞和空间转录学先进的分析工具.
研究的目的:
- 为了介绍LnCeCell 2.0,这是由单细胞和空间转录组学数据获得的lncRNA-ceRNA网络的更新和扩展资源.
- 提供细胞特异性和空间点特异性ceRNA相互作用,lncRNA生物标记物和相关临床信息的全面集合.
- 开发并提供一套网络工具,用于研究单细胞/点位分辨率的ceRNA调控机制.
主要方法:
- 整合了257个单细胞RNA测序 (scRNA-seq) 和空间转录组学测序 (stRNA-seq) 数据集.
- 构建细胞特异性和空间点特异性ceRNA相互作用和功能网络.
- 手动策划用于详细注释细胞类型,状态和ceRNAs的细胞下/细胞外位置.
- 开发24个网络工具,包括CeCellTraject,用于分析ceRNA网络和轨迹.
主要成果:
- LnCeCell 2.0 涵盖了来自 257 个数据集的 836,581 个 ceRNA 相互作用,跨越 1,002,988 个细胞和 367,971 个空间点.
- 该数据库包括15489个经过实验支持的lncRNA生物标志物和20326名癌症患者的临床数据.
- 开发的工具允许详细探索ceRNA分布和在单细胞/点分辨率下网络的动态变化.
结论:
- LnCeCell 2.0 显著增强了 lncRNA-ceRNA 网络的研究,具有前所未有的单细胞和空间分辨率.
- 该资源和相关工具有助于更深入地了解健康和疾病的监管机制.
- 这个更新的平台将加速研究ceRNAs在复杂生物系统中的复杂作用.
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