ViRBase: a resource for virus–host ncRNA-associated interactions

Abstract

Increasing evidence reveals that diverse non-coding RNAs (ncRNAs) play critically important roles in viral infection. Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to the completion of the viral life cycle. Many host cellular ncRNAs can also directly or indirectly influence viral replication and even target virus genomes. ViRBase (http://www.rna-society.org/virbase) aims to provide the scientific community with a resource for efficient browsing and visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection. The current version of ViRBase documents more than 12 000 viral and cellular ncRNA-associated virus–virus, virus–host, host–virus and host–host interactions involving more than 460 non-redundant ncRNAs and 4400 protein-coding genes from between more than 60 viruses and 20 hosts. Users can query, browse and manipulate these virus–host ncRNA-associated interactions. ViRBase will be of help in uncovering the generic organizing principles of cellular virus–host ncRNA-associated interaction networks in viral infection.

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

“…The relevant hits were downloaded and prepared systematically for further manual data curation. Second, RAID v2.0 integrated diverse RNA-associated interactions from other 18 databases, including ChIPBase (10), LncRNA2Target (11), LncRNAdisease (7), miR2Disease (12), miRTarBase (13), MNDR (14), ncRDeathDB (8), NPInter (15), OncomiRDB (16), sRNATarBase (17), StarBase (6), TransmiR (18) and ViRBase (19) as well as five computational prediction databases (DroID (20), EIMMo (21), miRanda (22), miRDB (23) and TargetScan (9)).…”

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases

“…To ensure a high quality database, we referred to the steps used to assemble the databases HMDD, Lnc2Cancer and ViRBase (11,13,18). We mainly applied the following three steps in the data collection process: collecting disease and ncRNA information, searching for relevant articles and extracting useful information from the selected articles.…”

“…We also applied the ncRNA category names for those and other ncRNAs, such as ribosomal RNA and transfer RNA. Second, we used a simple script to select all abstracts in the PubMed database using the following keyword combinations: ‘each nervous system disease’ and/or ‘each ncRNA symbol’ or ‘ncRNA category name’ (18). Then, we downloaded all published literature and available supplementary files describing the associations between NSDs and ncRNAs.…”

Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response

“…This collection represented the first coordinated effort to create a systems level description of host-pathogen interactions using multiple viral strains, host models, and '-omics' technologies. Systems biology approaches has been used by Katze laboratory in depth, and their research is focused to define and model virus-host interactions, innate immune signaling, and the varied strategies used by viruses; (Wang et al, 2009;Law et al, 2013;Josset et al, 2013;Cheung et al, 2012;Diamond et al, 2012;Navare et al, 2012;Aderem et al, 2011;Li et al, 2015;Murali et al, 2011;Rasmussen et al, 2011).…”