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The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function

Author

Listed:
  • Panagiotis Alexiou
  • Manolis Maragkakis
  • Giorgio L Papadopoulos
  • Victor A Simmosis
  • Lin Zhang
  • Artemis G Hatzigeorgiou

Abstract

Background: High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer. Methodology/Principal Findings: Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 3′ untranslated region (3′UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data. Conclusions/Significance: On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.

Suggested Citation

  • Panagiotis Alexiou & Manolis Maragkakis & Giorgio L Papadopoulos & Victor A Simmosis & Lin Zhang & Artemis G Hatzigeorgiou, 2010. "The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function," PLOS ONE, Public Library of Science, vol. 5(2), pages 1-7, February.
    • Handle: RePEc:plo:pone00:0009171
    DOI: 10.1371/journal.pone.0009171
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    1. Lee P. Lim & Nelson C. Lau & Philip Garrett-Engele & Andrew Grimson & Janell M. Schelter & John Castle & David P. Bartel & Peter S. Linsley & Jason M. Johnson, 2005. "Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs," Nature, Nature, vol. 433(7027), pages 769-773, February.
    2. Matthias Selbach & Björn Schwanhäusser & Nadine Thierfelder & Zhuo Fang & Raya Khanin & Nikolaus Rajewsky, 2008. "Widespread changes in protein synthesis induced by microRNAs," Nature, Nature, vol. 455(7209), pages 58-63, September.
    3. Ran Elkon & Reuven Agami, 2008. "Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs," PLOS Computational Biology, Public Library of Science, vol. 4(10), pages 1-10, October.
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