LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations

Abstract

LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA-protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts.

Figure 1.

Data contents and organization in LncBook 2.0. A comprehensive, high-quality collection of human lncRNAs is annotated at different omics levels and organized with user-friendly web interfaces for searching, browsing, visualizing, analyzing and downloading.

Figure 2.

Screenshot of ‘Genes’ page. Multi-omics features including expression capacity, featured expression pattern, featured methylation pattern, disease/trait-associated variation, lncRNA–protein interaction, and small protein expression, are summarized in a table, which enables customized filtration and sort. Functional evidences for SATB2-AS1 and WT1-AS inferred from multi-omics association analysis and experimental evidences are described in the manuscript.