College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
Nucleic Acids Res. 2021 Jan 8;49(D1):D125-D133. doi: 10.1093/nar/gkaa1017.
Within the tumour microenvironment, cells exhibit different behaviours driven by fine-tuning of gene regulation. Identification of cellular-specific gene regulatory networks will deepen the understanding of disease pathology at single-cell resolution and contribute to the development of precision medicine. Here, we describe a database, LnCeCell (http://www.bio-bigdata.net/LnCeCell/ or http://bio-bigdata.hrbmu.edu.cn/LnCeCell/), which aims to document cellular-specific long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) networks for personalised characterisation of diseases based on the 'One Cell, One World' theory. LnCeCell is curated with cellular-specific ceRNA regulations from >94 000 cells across 25 types of cancers and provides >9000 experimentally supported lncRNA biomarkers, associated with tumour metastasis, recurrence, prognosis, circulation, drug resistance, etc. For each cell, LnCeCell illustrates a global map of ceRNA sub-cellular locations, which have been manually curated from the literature and related data sources, and portrays a functional state atlas for a single cancer cell. LnCeCell also provides several flexible tools to infer ceRNA functions based on a specific cellular background. LnCeCell serves as an important resource for investigating the gene regulatory networks within a single cell and can help researchers understand the regulatory mechanisms underlying complex microbial ecosystems and individual phenotypes.
在肿瘤微环境中，细胞表现出不同的行为，这是由基因调控的精细调整驱动的。鉴定细胞特异性基因调控网络将加深对单细胞分辨率下疾病病理学的理解，并有助于精准医学的发展。在这里，我们描述了一个数据库，LnCeCell（http://www.bio-bigdata.net/LnCeCell/或http://bio-bigdata.hrbmu.edu.cn/LnCeCell/），其旨在基于“One Cell, One World”理论，为个性化疾病特征描述记录细胞特异性长非编码 RNA（lncRNA）相关竞争内源性 RNA（ceRNA）网络。LnCeCell 是从超过 25 种癌症的>94000 种细胞中精心挑选出的细胞特异性 ceRNA 调控，并提供了>9000 个经过实验支持的与肿瘤转移、复发、预后、循环、耐药性等相关的 lncRNA 生物标志物。对于每个细胞，LnCeCell 都展示了 ceRNA 亚细胞位置的全球图谱，这些图谱是从文献和相关数据源中手动整理的，并描绘了单个癌细胞的功能状态图谱。LnCeCell 还提供了几个灵活的工具，可根据特定的细胞背景推断 ceRNA 的功能。LnCeCell 是研究单个细胞内基因调控网络的重要资源，可帮助研究人员了解复杂微生物生态系统和个体表型背后的调控机制。
