Skip to main content

The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear

  • Conference paper
  • First Online:
Advances in Computational Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 680))

  • 2470 Accesses

Abstract

The biomedical literature has always played a critical role in the development of hypotheses to test, experimental design, and the analysis of study results. Yet, the ever-expanding body of biomedical literature is starting to present new challenges, in which locating pertinent literature from among the millions of published research articles is often a challenging task. A regular expression-based pattern matching method has been developed to profile the various gene and protein factors that may play a role in various tissues contained within an organism. This methodology has been demonstrated through the profiling of the various factors that are involved in the development of the inner ear, and is shown to be both effective and accurate.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. T. S. Gardner, D. di Bernardo, D. Lorenz, and J. J. Collins, “Inferring genetic networks and identifying compound mode of action via expression profiling,” Science, vol. 301, pp. 102–105, 2003.

    Article  PubMed  CAS  Google Scholar 

  2. G. S. Chaga, “Antibody arrays for determination of relative protein abundances,” Meth Mol Biol, vol. 441, pp. 129–151, 2008.

    Article  CAS  Google Scholar 

  3. M. Schena, D. Shalon, R. W. Davis, and P. O. Brown, “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science, vol. 270, pp. 467–470, 1995.

    Article  PubMed  CAS  Google Scholar 

  4. D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. Dicuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer, W. Helmberg, Y. Kapustin, O. Khovayko, D. Landsman, D. J. Lipman, T. L. Madden, D. R. Maglott, V. Miller, J. Ostell, K. D. Pruitt, G. D. Schuler, M. Shumway, E. Sequeira, S. T. Sherry, K. Sirotkin, A. Souvorov, G. Starchenko, R. L. Tatusov, T. A. Tatusova, L. Wagner, and E. Yaschenko, “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Res, vol. 36, pp. D13–D21, 2008.

    Article  PubMed  CAS  Google Scholar 

  5. J. E. Leonard, J. B. Colombe, and J. L. Levy, “Finding relevant references to genes and proteins in Medline using a Bayesian approach,” Bioinformatics, vol. 18, pp. 1515–1522, 2002.

    Article  PubMed  CAS  Google Scholar 

  6. M. Yoshida, K. Fukuda, and T. Takagi, “PNAD-CSS: A workbench for constructing a protein name abbreviation dictionary,” Bioinformatics, vol. 16, pp. 169–175, 2000.

    Article  PubMed  CAS  Google Scholar 

  7. M. A. Andrade, and P. Bork, “Automated extraction of information in molecular biology,” FEBS Lett, vol. 476, pp. 12–17, 2000.

    Article  PubMed  CAS  Google Scholar 

  8. F. Horn, A. L. Lau, and F. E. Cohen, “Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors,” Bioinformatics, vol. 20, pp. 557–568, 2004.

    Article  PubMed  CAS  Google Scholar 

  9. C.M. Frenz, Pro Perl Parsing. Berkeley, CA: Apress, 2005.

    Google Scholar 

  10. C. M. Frenz, “Deafness mutation mining using regular expression based pattern matching,” BMC Med Inform Decis Mak, vol. 7, p. 32, 2007.

    Article  PubMed  Google Scholar 

  11. G. Lawoko-Kerali, M. N. Rivolta, and M. Holley, “Expression of the transcription factors GATA3 and Pax2 during development of the mammalian inner ear,” J Comp Neurol, vol. 442, pp. 378–391, 2002.

    Article  PubMed  CAS  Google Scholar 

  12. L. M. Friedman, A. A. Dror, and K. B. Avraham, “Mouse models to study inner ear development and hereditary hearing loss,” Int J Dev Biol, vol. 51, pp. 609–631, 2007.

    Article  PubMed  CAS  Google Scholar 

  13. S. J. Harvey, R. Mount, Y. Sado, I. Naito, Y. Ninomiya, R. Harrison, B. Jefferson, R. Jacobs, and P. S. Thorner, “The inner ear of dogs with X-linked nephritis provides clues to the pathogenesis of hearing loss in X-linked Alport syndrome,” Am J Pathol, vol. 159, pp. 1097–1104, 2001.

    Article  PubMed  CAS  Google Scholar 

  14. T. J. Wright, E. P. Hatch, H. Karabagli, P. Karabagli, G. C. Schoenwolf, and S. L. Mansour, “Expression of mouse fibroblast growth factor and fibroblast growth factor receptor genes during early inner ear development,” Dev Dyn, vol. 228, pp. 267–272, 2003.

    Article  PubMed  CAS  Google Scholar 

  15. D. A. Frenz, W. Liu, J. D. Williams, V. Hatcher, V. Galinovic-Schwartz, K. C. Flanders, and T. R. Van de Water, “Induction of chondrogenesis: requirement for synergistic interaction of basic fibroblast growth factor and transforming growth factor-beta,” Development, vol. 120, pp. 415–424, 1994.

    PubMed  CAS  Google Scholar 

  16. P. Caye-Thomasen, N. Wagner, B. Lidegaard Frederiksen, K. Asal, and J. Thomsen, “Erythropoietin and erythropoietin receptor expression in the guinea pig inner ear,” Hear Res, vol. 203, pp. 21–27, 2005.

    Article  PubMed  CAS  Google Scholar 

  17. T. W. Vogel, A. O. Vortmeyer, I. A. Lubensky, Y. S. Lee, M. Furuta, B. Ikejiri, H. J. Kim, R. R. Lonser, E. H. Oldfield, and Z. Zhuang, “Coexpression of erythropoietin and its receptor in endolymphatic sac tumors,” J Neurosurg, vol. 103, pp. 284–288, 2005.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Christopher M. Frenz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this paper

Cite this paper

Frenz, C.M., Frenz, D.A. (2010). The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear. In: Arabnia, H. (eds) Advances in Computational Biology. Advances in Experimental Medicine and Biology, vol 680. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5913-3_19

Download citation

Publish with us

Policies and ethics