RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

“…The molecular properties of RNAs are essential for understanding their potential phase behaviour. For each natural RNA, the description in NCBI ( 35 ), molecular function in Gene Ontology (GO) ( 40 ), subcellular localization in RNALocate ( 34 ), interaction neighbour in RNAinter ( 41 ) and associated disease in DisGeNET ( 42 ) and OMIM ( 43 ) were all integrated as RNA annotation information (Figure 1B ). Designed RNAs were divided into four subclasses based on sequence characteristics.…”

Section: Data Collection and Processingmentioning

confidence: 99%

“…For each LLPS experiment, a phase diagram is presented in a graphical form, if available. For the natural RNAs, which have extensive information, clicking on the RNA symbol will take the user to the RNA annotation page, which integrates RNA description ( 35 ), molecular function ( 40 ), subcellular location ( 34 ), RNA interaction network (top 100 extracted from RNAinter) ( 41 ) and associated diseases ( 42–43 ) (Figure 3D ). A detailed tutorial for the usage of the database can be found on the ‘Help’ page.…”

Section: Web Interfacementioning

confidence: 99%

RNAPhaSep: a resource of RNAs undergoing phase separation

Zhu

Cui

et al. 2021

Self Cite

Liquid-liquid phase separation (LLPS) partitions cellular contents, underlies the formation of membraneless organelles and plays essential biological roles. To date, most of the research on LLPS has focused on proteins, especially RNA-binding proteins. However, accumulating evidence has demonstrated that RNAs can also function as ‘scaffolds’ and play essential roles in seeding or nucleating the formation of granules. To better utilize the knowledge dispersed in published literature, we here introduce RNAPhaSep (http://www.rnaphasep.cn), a manually curated database of RNAs undergoing LLPS. It contains 1113 entries with experimentally validated RNA self-assembly or RNA and protein co-involved phase separation events. RNAPhaSep contains various types of information, including RNA information, protein information, phase separation experiment information and integrated annotation from multiple databases. RNAPhaSep provides a valuable resource for exploring the relationship between RNA properties and phase behaviour, and may further enhance our comprehensive understanding of LLPS in cellular functions and human diseases.

“…RNA annotations, ncRNA SNP information and ncRNA drug-related information were added to the ViRBase v3.0. Detailed information on RNA editing sites was obtained from DARNED ( 19 ), Lncediting ( 20 ) and RADAR ( 21 ), RNA subcellular localization from RNALocate v2.0 ( 22 ), RNA modification sites from RMBase v2.0 ( 23 ), ncRNA SNP information from LincSNP v3.0 ( 24 ) and miRNASNP-v3.0 ( 25 ) and ncRNA-drug related information from ncDR ( 26 ), NoncoRNA ( 27 ), NRDTD ( 28 ) and RNAInter ( 29 ). Transcript and protein sequences from Refseq ( 30 ) and miRBase ( 31 ) databases were added to ViRBase v3.0 as a means to represent target sites predicted by miRanda ( 32 ), RIsearch ( 33 ) or PRIdictor ( 34 ).…”

Section: Methodsmentioning

confidence: 99%

“…In ViRBase v3.0, virus and host ncRNA-associated interactions were derived from different evidence resources, such as data from experimental evidences or computational predictions. Similar to the miRTarBase and RNAInter databases ( 29 , 40 ), these data were divided into strong experimental evidence (e.g. RNA immunoprecipitation and luciferase reporter assay results), weak experimental evidence (e.g.…”

Section: Methodsmentioning

confidence: 99%

ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation

Cheng

Lin

et al. 2021

Self Cite

As a means to aid in the investigation of viral infection mechanisms and identification of more effective antivirus targets, the availability of a source which continually collects and updates information on the virus and host ncRNA-associated interaction resources is essential. Here, we update the ViRBase database to version 3.0 (http://www.virbase.org/ or http://www.rna-society.org/virbase/). This update represents a major revision: (i) the total number of interaction entries is now greater than 820,000, an approximately 70-fold increment, involving 116 virus and 36 host organisms, (ii) it supplements and provides more details on RNA annotations (including RNA editing, RNA localization and RNA modification), ncRNA SNP and ncRNA-drug related information and (iii) it provides two additional tools for predicting binding sites (IntaRNA and PRIdictor), a visual plug-in to display interactions and a website which is optimized for more practical and user-friendly operation. Overall, ViRBase v3.0 provides a more comprehensive resource for virus and host ncRNA-associated interactions enabling researchers a more effective means for investigation of viral infections.