Charting the expression landscape of human long non-coding RNAs across diverse biological contexts with LncExpDB 2.0

LncExpDB is a comprehensive expression database of human long non-coding RNAs (lncRNAs) across diverse biological contexts. Here, we present LncExpDB 2.0 (https://ngdc.cncb.ac.cn/lncexpdb/) with significant updates and enhancements as detailed below: (i) expansion of biological contexts from 9 to 15 by integrating immunotherapy, aging, metabolic diseases, neurodegenerative diseases, reproduction, and wound healing; (ii) identification of 44 752 highly expressed genes, 39 253 featured genes with function-linked expression patterns, and 35.19 million lncRNA–mRNA co-expression pairs; (iii) in-depth functional analyses of featured genes, such as correlation with tumor microenvironment, age-related expression profiles, and functional enrichment; (iv) deployment of new tools for exploring complex lncRNA–mRNA interactions and lncRNA–immune checkpoint correlation; and (v) development of a pipeline module with documented workflow and command-line instructions for reproducible expression profiling. Collectively, LncExpDB 2.0 provides a multi-context landscape of lncRNA expression and serves as a critical resource for functional exploration of the “dark matter” in the human genome.