Journal of Computing Science and Engineering

Korean Institute of Information Scientists and Engineers (한국정보과학회)
권호 표지
DOI QR코드

DOI QR Code

Development of a New Software Package for Processing and Analyzing DNA Microarray Images

  • Choi, Jin-Ho (Taejon Christian International School) ;
  • Choi, Hee-Jun (Department of Electronics and Computer Science, Air Force Academy)
  • Received : 2010.07.23
  • Accepted : 2010.09.20
  • Published : 2010.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

Microarray technology is an interdisciplinary technique that promises a revolutionary progress toward better health and improved quality of life. The paper focuses on the development of an efficient software package, equipped with already well-known methods; also some new methods are proposed that will allow the processing and analysis of thousands of genes on microarray images. The microarray analysis software package (called SmartArray), newly proposed in this paper verifies, through microarray analysis, dramatic changes in the mRNA, protein, and activity level in the rat retina during light deprivation, which have been demonstrated in previous biological experiments. The analysis results demonstrate that SmartArray can successfully find many changes in gene expression levels in each subarray and classify them according to their significance.

Keywords

References

  1. BioDiscovery, Inc. 2006. ImaGene User Manual. http://www.biodiscovery.com
  2. Clontech, Inc. 2007. AtlasImage 2.7 User Manual. http://www.clontech.com.
  3. DUGGAN, D. J., BITTNER, M., CHEN, Y., MELTZER, P., AND TRENT, J. M. 1999. Expression profiling using cDNA microarrays, Nature genetics supplement, 21, 10-14. https://doi.org/10.1038/4434
  4. SCHENA, M. 2003. Microarray, John Wiley & Sons.
  5. DEBOUCK, C. AND GOODFELLOW, P. N. 1999. DNA microarrays in drug discovery and development, Nature genetics supplement, 21, 48-50. https://doi.org/10.1038/4475
  6. DOZMOROV, L. AND CENTOLA, M. 2002. Bioinformatics. An associative analysis of gene expression array data.
  7. FOLEY, J., DAM, A. V., FEINER, S., AND HUGHES, J. 1992. Computer graphics, Addison-Wesley Publishing Company, Inc.
  8. GERHOLD, D., RUSHMORE, T., AND CASKEY, C. T. 1999. DNA chips: promising toys have become powerful tools, Trends Biochemistry Science 24, 5, 168-173. https://doi.org/10.1016/S0968-0004(99)01382-1
  9. HALL, W. C. 2001. Online Microarray Analysis, Master Thesis, Univ. of Louisville.
  10. JAGOTA, M. 2001. Microarray analysis and visualization. Bioinformatics, BAY press.
  11. LI, Q., FRALEY, C., BUMGARNER, R. E., YEUNG, K. Y., AND RAFTERY, A. E. 2005. Donuts Scratches and Blanks: Robust Model-Based Segmentation of Microarray Images. Bioinformatics, 21, 2875-2882. https://doi.org/10.1093/bioinformatics/bti447
  12. Mathworks, Inc. 2010. MATLAB Bioinformatics Toolbox 3 User Manual. http://www.mathworks.com.
  13. MDS, Inc. 2008. Axon GenePix Pro 7 Software User Guide. http://www.moleculardevices.com
  14. NIH. 2010. The MSCL Analyst's Toolbox User Guide. http://affylims.cit.nih.gov.
  15. NOVIKOV, E. AND BARILLOT, E. 2007. Software package for automatic microarray image analysis (MAIA). Bioinformatics 23, 639-640. https://doi.org/10.1093/bioinformatics/btl644
  16. SONKA, M., HLAVAC, C., AND BOYLE, R. 1999. Image processing, analysis, and machine vision, PWS Publishing Co.
  17. WESTHEAD, D. R., PARISH, J. H., AND TWYMAN, R. M. 2002. Bioinformatics, BIOS Scientific Publishers.
  18. WHITE, A. M., DALY, D. S., WILLSE, A. R., PROTIC, M., AND CHANDLER, D. P. 2005. Bioinformatics, Automated Microarray Image Analysis Toolbox for MATLAB. https://doi.org/10.1093/bioinformatics/bti576