Databases for lncRNAs: a comparative evaluation of emerging tools

Abstract

The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.

Keywords: databases; lncRNAs; noncoding RNAs.

FIGURE 1.

Overview of lncRNAs functions.

FIGURE 2.

Key lncRNA database aspects evaluated. The number of cubes associated with each aspect reflects relative amounts of content available in the databases investigated in this article.

FIGURE 3.

Organization of lncRNA database contents. LncRNAs display multiple annotations: ID corresponds to the lncRNA Identifier (Ensembl, Noncode, Refseq), Aliases (lncRNA name); lncRNAs can be defined as different biotypes (sense, antisense, bidirectional, intronic, and intergenic) and are transcribed from different DNA strands. (TF) transcription factors.

FIGURE 4.

Example of discrepancies across databases using the lncRNA Meg3 as query. Meg3 is related to the protein-coding gene Rtl1 in ChIPBase (A), whereas it is associated with Dlk1 in LNCipedia (B). (C) Representation of the MEG3 containing genomic region with the UCSC Genome browser. (D) Venn diagram showing overlap of microRNAs associated with Meg3 in LNCipedia, DIANA-LncBase, and the Functional lncRNA Database.