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. 2014 Jul;20(7):989-93.
doi: 10.1261/rna.044776.114. Epub 2014 May 6.

RAID: A Comprehensive Resource for Human RNA-associated (RNA-RNA/RNA-protein) Interaction

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Free PMC article

RAID: A Comprehensive Resource for Human RNA-associated (RNA-RNA/RNA-protein) Interaction

Xiaomeng Zhang et al. RNA. .
Free PMC article

Abstract

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network.

Keywords: RNA–RNA; RNA–protein; database; interaction.

Figures

FIGURE 1.
FIGURE 1.
The overview of RAID database.
FIGURE 2.
FIGURE 2.
A flowchart for retrieving RNA-associated interaction entry. (A) Four searching paths for retrieving the RNA-associated interaction. (B) The result of a representative database entry. (C) The detailed information for an RNA-associated interaction. In the result and detail pages, RAID linked each RNA/protein symbol and PMID to their corresponding databases.
FIGURE 3.
FIGURE 3.
Representative screenshots of the Binding and Network pages. (A) The Binding page: representing the predicted binding sites and/or constants. (B) The Network page: representing the interaction subnetwork of interacting RNA/protein.

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