Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014, Article ID 678971, 11 pages
http://dx.doi.org/10.1155/2014/678971
Research Article

Identification of Simple Sequence Repeat Biomarkers through Cross-Species Comparison in a Tag Cloud Representation

1Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan
2Graduate Institute of Basic Medical Science, China Medical University, Taichung City 40402, Taiwan
3Department of Computer Science and Information Engineering, Asia University, Taichung City 41354, Taiwan
4Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan
5Department of Computer Science and Information Engineering, Tamkang University, New Taipei City 25137, Taiwan

Received 22 November 2013; Revised 27 February 2014; Accepted 27 February 2014; Published 31 March 2014

Academic Editor: Jose C. Nacher

Copyright © 2014 Jhen-Li Huang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Charlesworth, P. Sniegowski, and W. Stephan, “The evolutionary dynamics of repetitive DNA in eukaryotes,” Nature, vol. 371, no. 6494, pp. 215–220, 1994. View at Publisher · View at Google Scholar · View at Scopus
  2. Y.-C. Li, A. B. Korol, T. Fahima, and E. Nevo, “Microsatellites within genes: structure, function, and evolution,” Molecular Biology and Evolution, vol. 21, no. 6, pp. 991–1007, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. J. R. Brouwer, R. Willemsen, and B. A. Oostra, “Microsatellite repeat instability and neurological disease,” Bioessays, vol. 31, no. 1, pp. 71–83, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. Y. C. Li, A. B. Korol, T. Fahima, A. Beiles, and E. Nevo, “Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review,” Molecular Ecology, vol. 11, no. 12, pp. 2453–2465, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Mundlos, F. Otto, C. Mundlos et al., “Mutations involving the transcription factor CBFA1 cause cleidocranial dysplasia,” Cell, vol. 89, no. 5, pp. 773–779, 1997. View at Google Scholar · View at Scopus
  6. H. Y. Zoghbi and H. T. Orr, “Glutamine repeats and neurodegeneration,” Annual Review of Neuroscience, vol. 23, pp. 217–247, 2000. View at Publisher · View at Google Scholar · View at Scopus
  7. C. L. Cheng, T. Q. Gao, Z. Wang, and D. D. Li, “Role of insulin/insulin-like growth factor 1 signaling pathway in longevity,” World Journal of Gastroenterology, vol. 11, no. 13, pp. 1891–1895, 2005. View at Google Scholar · View at Scopus
  8. K. A. Woods, C. Camacho-Hübner, D. Barter, A. J. L. Clark, and M. O. Savage, “Insulin-like growth factor I gene deletion causing intrauterine growth retardation and severe short stature,” Acta Paediatrica, vol. 86, no. 423, pp. 39–45, 1997. View at Google Scholar · View at Scopus
  9. N. B. Sutter, C. D. Bustamante, K. Chase et al., “A single IGF1 allele is a major determinant of small size in dogs,” Science, vol. 316, no. 5821, pp. 112–115, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Lohmann, J. Ziegler, and L. Tetzlaff, “Comparison of tag cloud layouts: task-related performance and visual exploration,” in Human-Computer Interaction—INTERACT 2009, vol. 5726 of Lecture Notes in Computer Science, pp. 392–404, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Hennig, D. Groth, and H. Lehrach, “Automated gene ontology annotation for anonymous sequence data,” Nucleic Acids Research, vol. 31, no. 13, pp. 3712–3715, 2003. View at Publisher · View at Google Scholar · View at Scopus
  13. B. M. Good, E. A. Kawas, B. Kuo, and M. D. Wilkinson, “iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website,” BMC Bioinformatics, vol. 7, article 534, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. S. A. Samarajiwa, S. Forster, K. Auchettl, and P. J. Hertzog, “INTERFEROME: the database of interferon regulated genes,” Nucleic Acids Research, vol. 37, no. 1, pp. D852–D857, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. F. Supek, M. Bošnjak, N. Škunca, and T. Šmuc, “Revigo summarizes and visualizes long lists of gene ontology terms,” PLoS ONE, vol. 6, no. 7, Article ID e21800, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. E. Birney, T. D. Andrews, P. Bevan et al., “An overview of Ensembl,” Genome Research, vol. 14, pp. 925–928, 2004. View at Publisher · View at Google Scholar
  17. C. M. Chen, C. C. Chen, T. H. Shih, T. W. Pai, C. H. Hu, and W. S. Tzou, “Efficient algorithms for identifying orthologous simple sequence repeats of disease genes,” Journal of Systems Science and Complexity, vol. 23, pp. 906–916, 2010. View at Google Scholar
  18. É. Nascimento, R. Martinez, A. R. Lopes et al., “Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studies,” Journal of Clinical Microbiology, vol. 42, no. 11, pp. 5007–5014, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Zimprich, A. Benet-Pagès, W. Struhal et al., “A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset parkinson disease,” The American Journal of Human Genetics, vol. 89, no. 1, pp. 168–175, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. D. V. Luquetti, A. V. Hing, M. J. Rieder, D. A. Nickerson, E. H. Turner, J. Smith et al., “Mandibulofacial dysostosis with microcephaly caused by EFTUD2 mutations: expanding the phenotype,” The American Journal of Medical Genetics A, vol. 161, pp. 108–113, 2013. View at Google Scholar
  21. M. A. Lines, L. Huang, J. Schwartzentruber et al., “Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly,” The American Journal of Human Genetics, vol. 90, no. 2, pp. 369–377, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. J. W. Fondon III and H. R. Garner, “Molecular origins of rapid and continuous morphological evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 52, pp. 18058–18063, 2004. View at Publisher · View at Google Scholar · View at Scopus
  23. M. E. MacDonald, C. M. Ambrose, M. P. Duyao et al., “A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes,” Cell, vol. 72, no. 6, pp. 971–983, 1993. View at Publisher · View at Google Scholar · View at Scopus