Advertisement

Comparing 2-D Electrophoretic Gels Across Internet Databases

An Open Source Application
  • Peter F. Lemkin
  • Gregory C. Thornwall
  • Jai Evans
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

In (1, 2, 3, 4) and in the previous edition of this book (5), we described a Web-based computer-assisted visual method called Flicker for comparing two-dimensional (2-D) protein gel images across the Internet using a Java applet. We originally used the flicker method in the GELLAB 2-D gel analysis system (6–x9 9). The applet (primarily for Web-based analysis using a Web browser) has since been converted to a Java standalone application that can run on a user’s computer. The new application also can access images from the Web but can now more easily access the user’s data on their local computer. The new version is available as open source on http://open2dprot.sourceforge.net/ Flicker, where the executable program and the source code are available. Some of the code was derived from the old Flicker applet program and some from the MicroArray Explorer (10)—an open-source data-mining tool for microarray analysis (http:// maexplorer.sourceforge.net/).

Keywords

Federate Database Lower Right Hand Corner Computing Window Keyboard Shortcut Menu Command 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Lemkin, P. F. (1997) Comparing two-dimensional electrophoretic gels across the Internet. Electrophoresis 18, 461–470.PubMedCrossRefGoogle Scholar
  2. 2.
    Lemkin, P. F. and Thornwall, G. (1999) Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database. Molecular Biotechnology 12, 159–172.PubMedCrossRefGoogle Scholar
  3. 3.
    Lemkin, P. F. (1997) 2DWG meta-database of 2D electrophoretic gel images on the Internet. Electrophoresis 18, 2759–2773.PubMedCrossRefGoogle Scholar
  4. 4.
    Lemkin, P. F. (1997) Comparing 2D electrophoretic gels across Internet databases. In: 2-D Protocols for Proteome Analysis, Methods in Molecular Biology, Vol. 112, Andrew Link (ed.), Humana Press, Totowa, NJ: 339–410.Google Scholar
  5. 5.
    Lemkin, P. F. and Thornwall, G (2002) Comparing 2D Electrophoretic gels across data-bases. In Protein Protocol Handbook, J. M. Walker (ed.), Humana Press, Totowa, NJ, pp 197–214.CrossRefGoogle Scholar
  6. 6.
    Lemkin, P. F., Merril, C., Lipkin, L., et al. (1979) Software aids for the analysis of 2D gel electrophoresis images. Comput Biomed Res. 12, 517–544.PubMedCrossRefGoogle Scholar
  7. 7.
    Lipkin, L. E. and Lemkin, P. F. (1980) Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. Clin Chem. 26, 1403–1412.PubMedGoogle Scholar
  8. 8.
    Lemkin, P. F. and Lester, E. P. (1989) Database and search techniques for two-dimen-sional gel protein data: a comparison of paradigms for exploratory data analysis and pros-pects for biological modeling. Electrophoresis 10, 122–140.PubMedCrossRefGoogle Scholar
  9. 9.
    Lester, E. P., Lemkin, P. F., Lowery, J. F., and Lipkin, L. E. (1982) Human leukemias: a preliminary 2-D electrophretic analysis. Electrophoresis 3, 364–375.CrossRefGoogle Scholar
  10. 10.
    Lemkin, P. F., Thornwall, G. C., Walton, K. D., and Hennighausen L. (2000) The Microarray Explorer tool for data mining of cDNA microarrays-application for the mam-mary gland. Nucleic Acids Research 28, 4452–4459.PubMedCrossRefGoogle Scholar
  11. 11.
    Herbert, B. R., Pederson, S. L., Harry, J. L., et al. (2003) Mastering genome complexity using two-dimensional gel electrophoresis. PharmaGenomics Sept, 22–36.Google Scholar
  12. 12.
    Hood, L. (2002) A personal view of molecular technology and how it has changed biology. J Proteome Biology 1, 399–409.CrossRefGoogle Scholar
  13. 13.
    Herbert, B. R., Pedersen, S. K., Harry, J. L., et al. (2003) Mastering proteome complexity using two-dimensional gel electrophoresis. PharmaGenomics 3, 21–36.Google Scholar
  14. 14.
    Pedersen, S. K., Harry, J. L., Sebastian, L., et al. (2003) Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins. J Proteome Biology 2, 303–311.CrossRefGoogle Scholar
  15. 15.
    Pieper, R., Su, Q., Gatlin, C. L., Huang, S.-T., Anderson, N.L., and Steiner, S. (2003) Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3, 422–432.PubMedCrossRefGoogle Scholar
  16. 16.
    Pieper, R., Gatlin, C. L., Makusky, A. J., et al. (2003) The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electro-phoresis gels and identification of 325 distinct proteins. Proteomics 3, 1345–1364.PubMedCrossRefGoogle Scholar
  17. 17.
    Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: history, charac-ter, and diagnostic prospects. J. Mol. Cellular Proteomics 1, 845–867.CrossRefGoogle Scholar
  18. 18.
    Liotta, L. A., Espina, V., Mehta, A. I., et al. (2003) Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 3, 317–325.PubMedCrossRefGoogle Scholar
  19. 19.
    Hoving, S,. Gerrits, B., Voshol, H., Muller, D., Roberts, R. C., and vanOostrum, J. (2002) Preparative two-dimensional gel electrophoresis at alkaline pH using narrow range immo-bilized pH gradients. Proteomics 2, 127–134.PubMedCrossRefGoogle Scholar
  20. 20.
    VonEggeling, F., Gawriljuk, A., Fiedler, W., et al. (2001) Fluorescent dual colour 2D-protein gel electrophoresis for rapid detection of differences in protein pattern with standard image analysis software. Int J Mol Med. 8, 373–377.Google Scholar
  21. 21.
    Lopez, M. F., Mikulskis, A., Golenko, E., et al. (2003) High-content proteomics: Fluorescence multiplexing using an integrated, high-sensitivity, multi-wavelength charge-coupled device imaging system. Proteomics 3, 1109–1116.PubMedCrossRefGoogle Scholar
  22. 22.
    Sanchez, J.-C., Appel, R. D., Golaz, O., et al. (1995) Inside SWISS-2DPAGE database. Electrophoresis 16, 1131–1151.PubMedCrossRefGoogle Scholar
  23. 23.
    Appel, R. D., Bairoch, A., Sanchez, J-C., et al. (1996). Federated two-dimensional electro-phoresis database: a simple means of publishing two-dimensional electrophoresis data. Electrophoresis 17, 540–546.PubMedCrossRefGoogle Scholar
  24. 24.
    Appel, R. D., Sanchez, J-C., Bairoch, A., et al. (1993) SWISS-2DPAGE: A database of two-dimensional gel electrophoresis images. Electrophoresis 14, 1232–1238.PubMedCrossRefGoogle Scholar
  25. 25.
    Appel, R. D., Sanchez, J.-C., Bairoch, A., et al. (1994) SWISS-2DPAGE database of two dimensional polyacrylamide gel electrophoresis. Nucleic Acids Res. 22(17), 3581–3582.PubMedGoogle Scholar
  26. 26.
    Arnold, K., and Gosling, J. (1996) The Java Programming Language. Addison Wesley, NY.Google Scholar
  27. 27.
    Wolberg, G. (1990) Digital Image Warping. IEEE Computer Press Monograph, Los Alamitos, CA.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Peter F. Lemkin
    • 1
  • Gregory C. Thornwall
    • 2
  • Jai Evans
    • 3
  1. 1.LECBNCI- FrederickFrederick
  2. 2.LECBSAIC FrederickFrederick
  3. 3.LECBCIT, NIHFrederick

Personalised recommendations