LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. Issue Volume 49:Issue D1(2021) (21st November 2020)

• Record Type: Journal Article
• Authors: Wang, Peng; Guo, Qiuyan; Hao, Yangyang; Liu, Qian; Gao, Yue; Zhi, Hui; Li, Xin; Shang, Shipeng; Guo, Shuang; Zhang, Yunpeng; Ning, Shangwei; Li, Xia
• Is Part Of: Nucleic acids research. Volume 49:Issue D1(2021)
• Page Start: D125
• Page End: D133
• Publication Date: 2020-11-21
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa1017
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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.