RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

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 RNAassociated 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.

RNALocate: a resource for RNA subcellular localizations

“…More than 9200 RNAs with orthology/paralogy from miRBase and Homologene database have been provided in RNALocate for investigation on RNA subcellular localizations conservation. To further understand the interaction information between different RNAs in various types of subcellular localizations online, a ‘Network’ option has also been provided to visualize RNA interaction network with subcellular localization and organism (14,15). …”

RAID v2.0: an updated resource of RNA-associated interactions across organisms

“…Hence, in recent years, a wide variety of experimental and computational prediction techniques have expanded a number of diverse RNA-associated interaction data sets. Most of these interactions are available in a variety of databases (5–9), including several databases that primarily manually collect and curate diverse RNA-associated interactions with experimental evidence from literature. Other databases focus on a more generalized perspective for diverse RNAs and their partners in specific cellular processes.…”

“…Because the comprehensive regulation of crosstalk between diverse RNA and proteins still remains ambiguous, we updated the RAID database (5) to version 2.0 (RAID v2.0, http://www.rna-society.org/raid/) by integrating experimental and computational prediction interactions through the manual curation of the literature and another 18 resources under one common framework (Figure 1). Accordingly, RAID v2.0 will offer several distinctive advantages: (i) integration from numerous resources, including experimental and computational prediction databases as well as manual curation of the literature (recruiting more than 5.27 million RNA-associated interactions and exceeding an 850-fold increase over the previous version); (ii) provision of an integrative confidence score for each RNA-associated interaction, considering that an integrated scoring strategy will offer higher confidence when independent types of evidence agree; and (iii) mapping RNA-associated interactions into numerous species to facilitate studies of homology (increased coverage across 60 species).…”

RAIN: RNA–protein Association and Interaction Networks

“…This led to the generation of databases storing ncRNA interactions such as miRTarBase (6) and TarBase (7) containing microRNA (miRNA)–target interactions. NPInter (5), RAID (8) and StarBase (9) are examples of databases collecting interactions between ncRNAs and proteins.…”