LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution.

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.

• Authors: Peng Wang, Qiuyan Guo, Yangyang Hao, Qian Liu, Yue Gao, Hui Zhi, Xin Li, Shipeng Shang, Shuang Guo, Yunpeng Zhang, Shangwei Ning, Xia Li
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 49 Issue D1 Pg. D125-D133 (01 08 2021) ISSN: 1362-4962 [Electronic] England
• PMID: 33219686 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• Antineoplastic Agents
• Neoplasm Proteins
• RNA, Long Noncoding
• RNA, Neoplasm

Topics

• Antineoplastic Agents (therapeutic use)
• Cell Line, Tumor
• Databases, Genetic
• Drug Resistance, Neoplasm (genetics)
• Gene Expression Regulation, Neoplastic
• Gene Regulatory Networks
• Humans
• Internet
• Neoplasm Proteins (classification, genetics, metabolism)
• Neoplasms (diagnosis, drug therapy, genetics, pathology)
• Prognosis
• RNA, Long Noncoding (classification, genetics, metabolism)
• RNA, Neoplasm (classification, genetics, metabolism)
• Recurrence
• Signal Transduction
• Software
• Tumor Microenvironment (genetics)