IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0009171.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009171
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0009171&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0009171?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Urmo Võsa & Tõnu Esko & Silva Kasela & Tarmo Annilo, 2015. "Altered Gene Expression Associated with microRNA Binding Site Polymorphisms," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-24, October.
    2. Evelyn Zacharewicz & Paul Della Gatta & John Reynolds & Andrew Garnham & Tamsyn Crowley & Aaron P Russell & Séverine Lamon, 2014. "Identification of MicroRNAs Linked to Regulators of Muscle Protein Synthesis and Regeneration in Young and Old Skeletal Muscle," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-25, December.
    3. David Lyon & Maria Angeles Castillejo & Christiana Staudinger & Wolfram Weckwerth & Stefanie Wienkoop & Volker Egelhofer, 2014. "Automated Protein Turnover Calculations from 15N Partial Metabolic Labeling LC/MS Shotgun Proteomics Data," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-10, April.
    4. Alicia Hurtado & Irene Mota-Gómez & Miguel Lao & Francisca M. Real & Johanna Jedamzick & Miguel Burgos & Darío G. Lupiáñez & Rafael Jiménez & Francisco J. Barrionuevo, 2024. "Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    5. W.L. Bai & Y.L. Dang & R.H. Yin & R.L. Yin & W.Q. Jiang & Z.Y. Wang & Y.B. Zhu & J.J. Wang & Z.H. Zhao & G.B. Luo, 2016. "Combination of let-7d-5p, miR-26a-5p, and miR-15a-5p is suitable normalizer for studying microRNA expression in skin tissue of Liaoning cashmere goat during hair follicle cycle," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 61(3), pages 99-107.
    6. Adam A Margolin & Shao-En Ong & Monica Schenone & Robert Gould & Stuart L Schreiber & Steven A Carr & Todd R Golub, 2009. "Empirical Bayes Analysis of Quantitative Proteomics Experiments," PLOS ONE, Public Library of Science, vol. 4(10), pages 1-15, October.
    7. Chikako Ragan & Michael Zuker & Mark A Ragan, 2011. "Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-11, February.
    8. Peng Wang & Shangwei Ning & Qianghu Wang & Ronghong Li & Jingrun Ye & Zuxianglan Zhao & Yan Li & Teng Huang & Xia Li, 2013. "mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data," PLOS ONE, Public Library of Science, vol. 8(1), pages 1-12, January.
    9. Ramkrishna Mitra & Sanghamitra Bandyopadhyay, 2011. "MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-13, September.
    10. Wenliang Zhu & Xuan Kan, 2014. "Neural Network Cascade Optimizes MicroRNA Biomarker Selection for Nasopharyngeal Cancer Prognosis," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-7, October.
    11. Yuheng Lu & Christina S Leslie, 2016. "Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-18, July.
    12. Wenjie Zhu & Binghe Xu, 2014. "MicroRNA-21 Identified as Predictor of Cancer Outcome: A Meta-Analysis," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-7, August.
    13. Parawee Lekprasert & Michael Mayhew & Uwe Ohler, 2011. "Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-13, June.
    14. Weina Xu & Jinyi Liu & Huan Qi & Ruolin Si & Zhiguang Zhao & Zhiju Tao & Yuchuan Bai & Shipeng Hu & Xiaohan Sun & Yulin Cong & Haoye Zhang & Duchangjiang Fan & Long Xiao & Yangyang Wang & Yongbin Li &, 2024. "A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    15. Ho Thi Bich Phuong & Vien Ngoc Thach & Luong Hoang Ngan & Le Thi Truc Linh, 2018. "Using Bioinformatics to predict potential targets of Microrna-144 in osteoarthritis," HO CHI MINH CITY OPEN UNIVERSITY JOURNAL OF SCIENCE - ENGINEERING AND TECHNOLOGY, HO CHI MINH CITY OPEN UNIVERSITY JOURNAL OF SCIENCE, HO CHI MINH CITY OPEN UNIVERSITY, vol. 8(1), pages 43-52.
    16. Rachel A Hillmer, 2015. "Systems Biology for Biologists," PLOS Pathogens, Public Library of Science, vol. 11(5), pages 1-6, May.
    17. Joel W Graff & Linda S Powers & Anne M Dickson & Jongkwang Kim & Anna C Reisetter & Ihab H Hassan & Karol Kremens & Thomas J Gross & Mary E Wilson & Martha M Monick, 2012. "Cigarette Smoking Decreases Global MicroRNA Expression in Human Alveolar Macrophages," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-13, August.
    18. Jana Zecha & Wassim Gabriel & Ria Spallek & Yun-Chien Chang & Julia Mergner & Mathias Wilhelm & Florian Bassermann & Bernhard Kuster, 2022. "Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    19. Zhdanov, Vladimir P., 2010. "ncRNA-mediated bistability in the synthesis of hundreds of distinct mRNAs and proteins," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(4), pages 887-890.
    20. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0009171. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.