ViRBase


NAR Molecular Biology Database Collection entry number 1791
Yanhui Li; Changliang Wang; Zhengqiang Miao; Xiaoman Bi; Deng Wu; Nana Jin; Liqiang Wang; Hao Wu; Kun Qian; Chunhua Li; Ting Zhang; Chunrui Zhang; Ying Yi; Hongyan Lai; Yongfei Hu; Lixin Cheng; Kwong-Sak Leung; Xiaobo Li; Fengmin Zhang; Kongning Li; Xia Li; Dong Wang

Database Description

Increasing evidence reveals that diverse non-coding RNAs (ncRNAs) play critically important roles in viral infection [1-3]. Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to completion of the viral life cycle. Many host cellular ncRNAs can also directly or indirectly influence viral replication and even target virus genomes [2,4]. 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 over 12000 viral and cellular ncRNA-associated virus-virus, virus-host, host-virus and host-host interactions by manually curating the literatures, involving more than 60 different viruses and 20 hosts. Most medically relevant viruses are contained within the database, including EBV, HIV-1, HBV, HCV, H1N1, H3N2, KSHV. Researchers can follow these interactions to explore how the virus-host ncRNA-associated interaction network is organized. The whole dataset can be easily queried and downloaded through the webpage, and visualization tools embedding the Cytoscape web tool for interactively browsing and analyzing the dataset are provided. ViRBase also provides 5 options on the “Help” page to provide instructions for using the database. In addition, the identification of RNA-associated binding sites can provide valuable insights into the underlying regulatory mechanisms of various ncRNAs, thus ViRBase also incorporates several useful tools to analyze the predicted binding site information for these interactions.

Acknowledgements

We thank all student for the data collection, annotation and web-page development. ViRBase is supported by National High Technology Research and Development Program of China , Major State Basic Research Development Program of China, National Natural Science Foundation of China, China Postdoctoral Science Foundation funded project, Heilongjiang Postdoctoral Foundation, Scientific Research Fund of Heilongjiang Provincial Education Department .

References

1. Skalsky, R.L. and Cullen, B.R. (2010) Viruses, microRNAs, and host interactions. Annu Rev Microbiol, 64, 123-141.
2. Gottwein, E. and Cullen, B.R. (2008) Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe, 3, 375-387.
3. Ghosh, Z., Mallick, B. and Chakrabarti, J. (2009) Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res, 37, 1035-1048.
4. Klase, Z., Houzet, L. and Jeang, K.T. (2012) MicroRNAs and HIV-1: complex interactions. J Biol Chem, 287, 40884-40890.


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