VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets

Abstract

Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus. Hence, miRNAs play a key role in host-virus interactions and pathogenesis of viral diseases. Lately, miRNAs have also shown potential as important targets for the development of novel antiviral therapeutics. Although several miRNA and their target repositories are available for human and other organisms in literature, but a dedicated resource on viral miRNAs and their targets are lacking. Therefore, we have developed a comprehensive viral miRNA resource harboring information of 9133 entries in three subdatabases. This includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA ' VIRMIRNA: ' and 7283 of their target genes in ' VIRMIRTAR': . Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA ' AVIRMIR': . The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and useful analysis tools are also provided on the web interface. VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics. Database URL: http://crdd.osdd.net/servers/virmirna.

Figure 1.

VIRmiRNA architecture.

Figure 2.

VIRmiRNA statistics: Pie charts (a–c) representing statistical distribution of cell lines and bar graphs (d–f) depicting the statistical trend of experimental methods used in the three subdatabases viz VIRmiRNA, VIRmiRtar and AVIRmiR, respectively. NGS, next generation sequencing; RT-PCR, real-time PCR; CLIP, cross-linking immunoprecipitation.

Figure 3.

Schematic representation of the search output (a) a screenshot of search output returned in the tabular form having information regarding KSHV miRNAs, (b) Detailed information of kshv-miR-k12-2* miRNA, (c) and its interaction partners in graphical view.