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. 2020 Jan 8;48(D1):D189-D197.
doi: 10.1093/nar/gkz804.

RNAInter in 2020: RNA Interactome Repository With Increased Coverage and Annotation

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Free PMC article

RNAInter in 2020: RNA Interactome Repository With Increased Coverage and Annotation

Yunqing Lin et al. Nucleic Acids Res. .
Free PMC article

Abstract

Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.

Figures

Figure 1.
Figure 1.
Overview of the RNAInter database.
Figure 2.
Figure 2.
Statistics on RNAInter. (A) The distribution of five interaction types (RCI/RDI/RHI/RPI/RRI) in 22 RNA categories. The category ‘other RNA’ includes eRNA, ncRNA, others, repeats, ribozyme, scaRNA, scRNA, shRNA, sncRNA sRNA, unassigned RNA and unknown. (B) Number of interactions in vertebrata, nematoda, virus, arthropoda, fungi, viridiplantae, actiniaria, bacteria (left) and 28 species belonging to vertebrata (right).
Figure 3.
Figure 3.
New search function and data visualization of the RNA interactome. (A) Presentation of exact, fuzzy and batch search described in the search options. (B) Visualization of the interaction network, RNA structure and RNA dynamic expression.
Figure 4.
Figure 4.
Snapshot of four RNA interactome tools in RNAInter: RIscoper, PRIdictor, IntaRNA and DeepBind (left: input option, right: result presentation).

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