Browse predicted human virus miRNA targets Browse predited mouse virus miRNA targets Browse predited rat virus miRNA targets Browse predited chicken virus miRNA targets
Introduction Developers Softwares Databases Reference

Introduction

  What is ViTa ?

ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also provide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons. Additionally, a multiple functions and graphical web interface are designed and implemented to help users to investigate the microRNA roles in viral existence. ViTa is developed by Bidlab(2005), and will be maintain and update. More and more disease is supported in future.
Data Generation Flow miRNAs are produced from viruses Virus can produce miRNAs after infecting. The main function may escape host T cell, and reduce its expression, but not infective activity, and exist synchronous. For example, HIV is a famous virus which causes AIDS, can encode nef miRNAs that repress HIV's T antigen, but maintain its' infection.
Relationship between miRNA and virus
    MicroRNAs have multiple roles in regulation 
  of post-transcripts, which are ~ 22 nt long non-coding RNAs 
  found in all metazoan eukaryotes. Now, miRNAs are also produced
  from and viruses in mammalian. The possible role
  is to assist in escaping from host immunity mechanism by decreasing
  its activity (Omoto, Ito et al. 2004) or regulating host mRNAs. 
  Under powerful function of microRNAs/siRNAs in mammals, we try to 
  collect virus data from other databases, and predict putative 
  miRNAs on viruses to look for potential relationships between
  existence of influenza viruses and miRNAs, which are produced
  from its own or helper viruses.   

Infection of HIV
						
 Why to find host miRNA targets on virus ?
       Recently, miRNAs are discovered to affect viral existence by targeting to viruses after entering hosts, 
   such as hepatitis C virus(Jopling, Yi et al. 2005) and HIV(Hariharan, Scaria et al. 2005). Human miR-122a 
   appears to assist HCV replicate in host by targeting to 3íŽ UTR on HCV genome. Oppositely, HIV is suppressed
   by targeting several genes by human microRNAs. These tell us human microRNAs as regulators for affecting
   life cycle of viruses in host. And the relationship between viruses and host miRNAs is worthy to further
   research for potential therapy.  

Application The database will be developed as follows. (i) It will be made to support miRNA annotations including miRNA genes and miRNA targets on viruses for other hosts, not only human, mouse, rat and chicken; (ii) The ViTa data will be further analyzed to support the miRNAs involved in the combinatorial control of the expression of infecting viruses. (iii) A complete relationship between viruses and diseases are contained later.
Developers
Dr.Hsien-Da Huang

Softwares Databases
miRanda
TargetScan

 

ICTVdB
miRNAMap
miRBase
VirGen
VBRC

Reference

   1. Ambros, V., B. Bartel, et al. (2003). "A uniform system for microRNA annotation." Rna 9(3): 277-9.
   Bartel, D. P. (2004). "MicroRNAs: genomics, biogenesis, mechanism, and function." Cell 116(2): 281-97.
   Buchen-Osmond, C. (2003). "The universal virus database ICTVdB." COMPUTING IN SCIENCE & ENGINEERING 
   5(3): 16-25.
   2. Griffiths-Jones, S. (2004). "The microRNA Registry." Nucleic Acids Res 32(Database issue): D109-11.
   3. Griffiths-Jones, S., R. J. Grocock, et al. (2006). "miRBase: microRNA sequences, targets and gene 
   nomenclature." Nucleic Acids Res 34(Database issue): D140-4.
   4. Hariharan, M., V. Scaria, et al. (2005). "Targets for human encoded microRNAs in HIV genes." Biochem 
   Biophys Res Commun 337(4): 1214-8.
   5. Hofacker, I. L. (2003). "Vienna RNA secondary structure server." Nucleic Acids Res 31(13): 3429-31.
   6. Hsu, P. W., H. D. Huang, et al. (2006). "miRNAMap: genomic maps of microRNA genes and their target 
   genes in mammalian genomes." Nucleic Acids Res 34(Database issue): D135-9.
   7. John, B., A. J. Enright, et al. (2004). "Human MicroRNA targets." PLoS Biol 2(11): e363.
   8. Jopling, C. L., M. Yi, et al. (2005). "Modulation of hepatitis C virus RNA abundance by a liver-
   specific MicroRNA." Science 309(5740): 1577-81.
   9. Krek, A., D. Grun, et al. (2005). "Combinatorial microRNA target predictions." Nat Genet 37(5): 495-
   500.
   10. Kulkarni-Kale, U., S. Bhosle, et al. (2004). "VirGen: a comprehensive viral genome resource." Nucleic 
   Acids Res 32(Database issue): D289-92.
   11. Lecellier, C. H., P. Dunoyer, et al. (2005). "A cellular microRNA mediates antiviral defense in human 
   cells." Science 308(5721): 557-60.
   12. Lefkowitz, E. J., C. Upton, et al. (2005). "Poxvirus Bioinformatics Resource Center: a comprehensive 
   Poxviridae informational and analytical resource." Nucleic Acids Res 33(Database issue): D311-6.
   13. Lewis, B. P., C. B. Burge, et al. (2005). "Conserved seed pairing, often flanked by adenosines, 
   indicates that thousands of human genes are microRNA targets." Cell 120(1): 15-20.
   14. Lewis, B. P., I. H. Shih, et al. (2003). "Prediction of mammalian microRNA targets." Cell 115(7): 787-98.
   Lu, J., G. Getz, et al. (2005). "MicroRNA expression profiles classify human cancers." Nature 435(7043):
   834-8.
   15. Neilson, J. R. and P. A. Sharp (2005). "Herpesviruses throw a curve ball: new insights into microRNA 
   biogenesis and evolution." Nat Methods 2(4): 252-4.
   16. Rehmsmeier, M., P. Steffen, et al. (2004). "Fast and effective prediction of microRNA/target duplexes."
   Rna 10(10): 1507-17.
   17. Thompson, J. D., D. G. Higgins, et al. (1994). "CLUSTAL W: improving the sensitivity of progressive 
   multiple sequence alignment through sequence weighting, position-specific gap penalties and weight 
   matrix choice." Nucleic Acids Res 22(22): 4673-80.
   18. Washietl, S., I. L. Hofacker, et al. (2005). "Fast and reliable prediction of noncoding RNAs." Proc 
   Natl Acad Sci U S A 102(7): 2454-9.
   19. Zuker, M. (2003). "Mfold web server for nucleic acid folding and hybridization prediction." Nucleic 
   Acids Res 31(13): 3406-15.

 

 

Department of Biological Science and Technology, Institute of Bioinformatics
National Chiao Tung University,Hsinchu, Taiwan
Contact with: bryan@mail.NCTU.edu.tw