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. 2017 Jan 4;45(D1):D115-D118.
doi: 10.1093/nar/gkw1052. Epub 2016 Nov 28.

RAID v2.0: An Updated Resource of RNA-associated Interactions Across Organisms

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Free PMC article

RAID v2.0: An Updated Resource of RNA-associated Interactions Across Organisms

Ying Yi et al. Nucleic Acids Res. .
Free PMC article

Abstract

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA-RNA interactions and more than 1.2 million RNA-protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species.

Figures

Figure 1.
Figure 1.
Flowchart of database construction and the statistics of RNA categories and interactions. (A) The overview of the RAID v2.0 database; (B) The percentage of diverse RNA categories in RAID v2.0 database; (C) The number of RNA–RNA/RNA–protein interactions for diverse RNA categories in RAID v2.0 database, the height of histogram transformed by log10.

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