NGDC Dec 16, 2020
Recently, researchers from the Beijing Institute of Genomics of Chinese Academy of Sciences / China National Center for Bioinformation have constructed an expression database of human long non-coding RNAs (lncRNAs) —— LncExpDB. This work was published with the title "LncExpDB: an expression database of human long non-coding RNAs" in the journal Nucleic Acids Research on Oct 12, 2020.
The human genome transcribes a large number of lncRNAs, which are extensively involved in a variety of essential biological processes and human diseases. While hundreds of thousands of human lncRNAs have been identified primarily attributable to the rapid development of high-throughput sequencing technology, only a small subset of them have been functionally characterized. As RNA-seq data provides the most direct evidence for identifying their potential functions across various biological conditions, it is desirable to have a dedicated expression database that comprehensively integrates expression profiles and systematically characterizes expression features of human lncRNAs.
To this end, LncExpDB, an expression database of human lncRNAs, was developed. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101,293 high-quality human lncRNA genes derived from 1,977 samples of 337 biological conditions across nine biological contexts (normal tissue/cell line, cancer tissue/cell line, subcellular localization, exosome, cell differentiation, preimplantation embryo, organ development, circadian rhythm and virus infection).
LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25,191 featured genes, and further obtains 28,443,865 lncRNA-mRNA interactions. Moreover, LncExpDB is equipped with user-friendly web interfaces, which enables interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.
This work was supported by CAS Strategic Priority Research Program, National Key Research and Development Program of China, Youth Innovation Promotion Association of Chinese Academy of Sciences, National Natural Science Foundation of China, etc.
Data curation and analysis workflow of LncExpDB (Image by NGDC)
Dr. MA Lina
Dr. ZHANG Zhang