Skip to main content
Springer Nature Link
Log in

Visualization of Functional Aspects of microRNA Regulatory Networks Using the Gene Ontology

  • Conference paper
Biological and Medical Data Analysis (ISBMDA 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4345))

Included in the following conference series:

  • 1180 Accesses

Abstract

The post-transcriptional regulation of genes by microRNAs (miRNAs) is a recently discovered mechanism of growing importance. To uncover functional relations between genes regulated by the same miRNA or groups of miRNAs we suggest the simultaneous visualization of the miRNA regulatory network and the Gene Ontology (GO) categories of the targeted genes. The miRNA regulatory network is shown using circular drawings and the GO is visualized using treemaps. The GO categories of the genes targeted by user-selected miRNAs are highlighted in the treemap showing the complete GO hierarchy or selected branches of it. With this visualization method patterns of reoccurring categories can easily identified supporting the discovery of the functional role of miRNAs. Executables for MS-Windows are available under www.ics.forth.gr/~reczko/isbmda06

This work was supported in part by INFOBIOMED code: IST-2002-507585 and the Greek General Secretariat for Research and Technology under Program ”ARISTEIA”, Code 1308/B1/3.3.1/317/12.04.2002.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Lee, R.C., et al.: C. elegans heterochronic gene lin-4 encodes small rnas with antisense complementarity to lin-14. Cell 75, 843–854 (1993)

    Article  Google Scholar 

  2. John, B., et al.: Human microrna targets. PLoS Biology 2, e363 (2004)

    Article  Google Scholar 

  3. Enright, A.J., et al.: Microrna targets in drosophila. Genome Biol. 5, R1 (2003)

    Article  Google Scholar 

  4. Stark, A., et al.: Identification of drosophila microrna targets. PLoS Biology 1, E60 (2003)

    Article  Google Scholar 

  5. Lewis, B.P., et al.: Prediction of mammalian microrna targets. Cell 115, 787–798 (2003)

    Article  Google Scholar 

  6. Pfeffer, S., et al.: Identification of virus encoded micrornas. Science 304, 734–736 (2004)

    Article  Google Scholar 

  7. Kiriakidou, M., et al.: A combined computational-experimental approach predicts human microrna targets. Genes dev. 18, 1165–1178 (2004)

    Article  Google Scholar 

  8. Grün, D., et al.: Microrna target predictions across seven drosophial species and comparison to mammalian targets. PLoS Comp. Biol. 1, e13 (2005)

    Article  Google Scholar 

  9. Krek, A., et al.: Combinatorial microrna target predictions. Nature Genetics 37, 495–500 (2005)

    Article  Google Scholar 

  10. Rehmsmeier, M., et al.: Fast and effective prediction of microrna/target duplexes. RNA 10, 1507–1517 (2004)

    Article  Google Scholar 

  11. http://www.geneontology.org

  12. Di Battista, G., et al.: Graph Drawing: Algorithms for the Visualization of Graphs. Prentice Hall, Englewood Cliffs (1999)

    MATH  Google Scholar 

  13. Garey, M.R., Johnson, D.S.: Crossing number is np-complete. SIAM J. Algebraic Discrete Methods 4, 312–316 (1983)

    Article  MATH  MathSciNet  Google Scholar 

  14. Eades, P., et al.: On an edge crossing problem. In: Proc. of the Ninth Australian Computer Science Conference, pp. 327–334. Australian National University (1986)

    Google Scholar 

  15. Eades, P., Kelly, D.: Heuristics for drawing 2-layered networks. Ars Combin. 21-A, 89–98 (1986)

    MathSciNet  Google Scholar 

  16. Eades, P., Wormald, N.: Edge crossings in drawings of bipartite graphs. Algorithmica 11(4), 379–403 (1994)

    Article  MATH  MathSciNet  Google Scholar 

  17. Mǎkinen, E.: Experiments on drawing 2-level hierarchical graphs. Inter. Journ. Comput. Math. 36, 175–181 (1990)

    Article  Google Scholar 

  18. May, M., Szkatula, K.: On the bipartite crossing number. Control Cybernet. 17, 85–98 (1988)

    MATH  Google Scholar 

  19. Di Battista, G., Tamassia, R.: Algorithms for plane representations of acyclic graphs. Theoret. Computation Scien. 61, 175–198 (1988)

    Article  MATH  Google Scholar 

  20. Di Battista, G., et al.: Constrained visibility representations of graphs. Informat. Process. Letters 41, 1–7 (1992)

    Article  MATH  Google Scholar 

  21. Sugiyama, K., et al.: Methods for visual understanding of hierarchical systems. IEEE, Trans. Syst. Man. Cybern. 11(2), 109–125 (1981)

    Article  MathSciNet  Google Scholar 

  22. Gschwind, D.J., Murtagh, T.P.: A Recursive Algorithm for Drawing Hierarchical Directed Graphs. Department of Computer Science, Williams College (1989)

    Google Scholar 

  23. Carpano, M.J.: Automatic display of hierarchized graphs for computer aided decision analysis. IEEE, Transact. Syst. Man. Cybern. 10(11), 705–715 (1980)

    Article  Google Scholar 

  24. Johnson, B., Shneiderman, B.: Treemaps: a space-filling approach to the visualization of hierarchical information structures. In: Proc. of the 2nd Intern. IEEE Visualization Conference, October 1991, pp. 284–291 (1991)

    Google Scholar 

  25. Shneiderman, B.: Tree visualization with tree-maps: A 2d space-filling approach. ACM Transactions on Graphics 11(1), 73–78 (1992)

    Article  Google Scholar 

  26. Bruls, D.M., et al.: Squarified treemaps. In: Proceedings of the joint Eurographics and IEEE TVCG Symposium on Visualization, October 2000, pp. 33–42 (2000)

    Google Scholar 

  27. http://llama.med.harvard.edu/~berriz/GoFishWelcome.html

  28. http://www.godatabase.org/cgi-bin/amigo/go.cgi

  29. http://cgap.nci.nih.gov/Genes/GOBrowser

  30. http://sourceforge.net/project/showfiles.php?group_id=36855

  31. Baehrecke, E.H., et al.: Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5 (2004)

    Google Scholar 

  32. McConnell, P., et al.: Applications of tree-maps to hierarchical biological data. Bioinformatics 18(9), 1278–1279 (2002)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Computer Science Department, University of Crete,  

    Alkiviadis Symeonidis, Ioannis G. Tollis & Martin Reczko

  2. Institute for Computer Science, Foundation for Research and Technology – Hellas, P.O. Box 1385, 711 10, Heraklion, Crete, Greece

    Alkiviadis Symeonidis & Ioannis G. Tollis

Authors
  1. Alkiviadis Symeonidis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ioannis G. Tollis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Martin Reczko
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. The Medical School, Lab of Medical Informatics, Aristotle University, Box 323, 54124, Thessaloniki, Greece

    Nicos Maglaveras  & Ioanna Chouvarda  & 

  2. Laboratory of Medical Informatics, Faculty of Medicine, Aristotle University of Thessaloniki, P.O.Box 323, 54124, Thessaloniki, Greece

    Vassilis Koutkias

  3. Institute of Informatics, Johann Wolfgang Goethe-Universität, 60054, Frankfurt a.M., Germany

    Rüdiger Brause

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Symeonidis, A., Tollis, I.G., Reczko, M. (2006). Visualization of Functional Aspects of microRNA Regulatory Networks Using the Gene Ontology. In: Maglaveras, N., Chouvarda, I., Koutkias, V., Brause, R. (eds) Biological and Medical Data Analysis. ISBMDA 2006. Lecture Notes in Computer Science(), vol 4345. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11946465_2

Download citation

  • DOI: https://doi.org/10.1007/11946465_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68063-5

  • Online ISBN: 978-3-540-68065-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics