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2D-PAGE Maps Analysis

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Clinical Proteomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 428))

Summary

Due to the low reproducibility affecting 2D gel-electrophoresis and the complex maps provided by this technique, the use of effective and robust methods for the comparison and classification of 2D maps is a fundamental tool for the development of automated diagnostic methods. A review of classical and recently developed methods for the comparison of 2D maps is presented here. The methods proposed regard both the analysis of spot volume datasets through multivariate statistical tools (pattern recognition methods, cluster analysis, and classification methods) and the analysis of 2D map images through fuzzy logic, three-way PCA, and the use of moment functions.

The theoretical basis of each procedure is briefly introduced, together with a review of the most interesting applications present in recent literature.

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References

  1. Mahon, P., Dupree, P., (2001) Quantitative and reproducible two-dimensional gel analysis using Phoretix 2D Full, Electrophoresis 22, 2075–2085

    Article  PubMed  CAS  Google Scholar 

  2. Rubinfeld, A., Keren-Lehrer, T., Hadas, G., Smilansky, Z., (2003) Hierarchical analysis of large-scale two-dimensional gel-electrophoresis experiments, Proteomics 3, 1930–1935

    Article  PubMed  CAS  Google Scholar 

  3. Anderson, N.L., Taylor, J., Scandora, A.E., Coulter, B.P., Anderson, N.G., (1981) The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns, Clinical Chemistry 27(11), 1807–1820

    PubMed  CAS  Google Scholar 

  4. Rosengren, A.T., Salmi, J.M., Aittokallio, T., Westerholm, J., Lahesmaa, R., Nyman, T.A., Nevalainen, O.S., (2003) Comparison of PDQuest and Progenesis software packages in the analysis of two dimensional electrophoresis gels, Proteomics 3, 1936–1946

    Article  PubMed  CAS  Google Scholar 

  5. Raman, B., Cheung, A., Marten, M.R., (2002) Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie, Electrophoresis 23, 2194–2202

    Article  PubMed  CAS  Google Scholar 

  6. Panek, J., Vohradsky, J., (1999) Point pattern matching in the analysis of two-dimensional gel electropherograms, Electrophoresis 20, 3483–3491

    Article  PubMed  CAS  Google Scholar 

  7. Pleissner, K.P., Hoffman, F., Kriegel, K., Wenk, C., Wegner, S., Sahistrom, A., Oswald, H., Alt, H., Fleck, E., (1999) New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases, Electrophoresis 20, 755–765

    Article  PubMed  CAS  Google Scholar 

  8. Voss, T., Haberl, P., (2000) Observations on the reproducibility and matching efficiency of two-dimensional electrophoresis gels: consequences for comprehensive data analysis, Electrophoresis 21, 3345–3350

    Article  PubMed  CAS  Google Scholar 

  9. Cutler, P., Heald, G., White, I.R., Ruan, J., (2003) A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection, Proteomics 3, 392–401

    Article  PubMed  CAS  Google Scholar 

  10. Molloy, M.P., Brzezinski, E.E., Hang, J., McDowell, M.T., VanBogelen, R.A., (2003) Overcoming technical variation and biological variation in quantitative proteomics, Proteomics 3 , 1912–1919

    Article  PubMed  CAS  Google Scholar 

  11. Moritz, B., Meyer, H.E., (2003) Approaches for the quantification of protein concentration ratios, Proteomics 3 , 2208–2220

    Article  PubMed  CAS  Google Scholar 

  12. Wheelock, A.M., Buckpitt, A.R., (2005) Software-induced variance in two-dimensional gel electrophoresis image analysis, Electrophoresis 26, 4508–4520

    Article  PubMed  CAS  Google Scholar 

  13. Almeida, J.S., Stanislaus, R., Krug, E., Arthur, J.M., (2005) Normalisation and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics, Proteomics 5, 1242–1249

    Article  PubMed  CAS  Google Scholar 

  14. Pietrogrande, M.C., Marchetti, N., Dondi, F., Righetti, P.G., (2003) Spot overlapping in two-dimensional polyacrylamide gel electrophoresis maps: relevance to proteomics, Electrophoresis 24, 217–224

    Article  PubMed  CAS  Google Scholar 

  15. Pietrogrande, M.C., Marchetti, N., Dondi, F., Righetti, P.G., (2002) Spot overlapping in two-dimensional polyacrylamide gel electrophoresis separations: a statistical study of complex protein maps, Electrophoresis 23, 283–291

    Article  PubMed  CAS  Google Scholar 

  16. Campostrini, N., Areces, L.B., Rappsilber, J., Pietrogrande M.C., Dondi, F., Pastorino, F., Ponzoni, M., Righetti, P.G., (2005) Spot overlapping in two-dimensional maps: a serious problem ignored for much too long, Proteomics 2005(5), 2385–2395

    Article  Google Scholar 

  17. Garrels, J.I., (1979) Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines, J. Biol. Chem. 254, 7961–7977

    PubMed  CAS  Google Scholar 

  18. Garrels, J.I., Farrar, J.T., Burwell IV, C.B., (1984) In: Celis, J.E., Bravo, R. (Eds.), Two-dimensional Gel Electrophoresis of Proteins, Academic Press, Orlando, FA, USA, pp. 38–91

    Google Scholar 

  19. Garrels, J.I., (1989) The QUEST system for quantitative analysis of two-dimensional gels, J. Biol. Chem. 264 , 5269–5282

    PubMed  CAS  Google Scholar 

  20. Massart, D.L., Vandeginste, B.G.M., Deming, S.M., Michotte, Y., Kaufman, L., (1988) Chemometrics: A Textbook. Amsterdam, Elsevier

    Google Scholar 

  21. Vandeginste, B.G.M., Massart, D.L., Buydens, L.M.C., De Jong, S., Lewi, P.J., Smeyers-Verbeke, J., (1998) Handbook of Chemometrics and Qualimetrics: Part B. Amsterdam, Elsevier

    Google Scholar 

  22. Marengo, E., Robotti, E., Righetti, P.G., Campostrini, N., Pascali, J., Ponzoni, M., (2004) Study of Proteomic changes associated with healthy and tumoral murine samples in Neuroblastoma by Principal Component Analysis and classification methods, Clinica Chimica Acta 345, 55–67

    Article  CAS  Google Scholar 

  23. Marengo, E., Robotti, E., Bobba, M., Liparota, M.C., Antonucci, F., Rustichelli, C., Zamò, A., Chilosi, M., Hamdan, M., Righetti, P.G., (2006) Characterisation of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel-electrophoresis and multivariate statistical tools, Electrophoresis 27, 484–494

    Article  PubMed  CAS  Google Scholar 

  24. Massart, D.L., Kaufman, L., (1983) In: Elving, P.J., Winefordner, J.D. (Eds.), The Interpretation of Analytical Chemical Data by the Use of Cluster Analysis. Wiley, New York, USA

    Google Scholar 

  25. Eisenbeis, R.A. (Ed.), (1972) Discriminant Analysis and Classification Procedures: Theory and Applications. Lexington, USA

    Google Scholar 

  26. Klecka, W.R. (Ed.), (1980) Discriminant Analysis. Sage Publications, Beverly Hills, USA

    Google Scholar 

  27. Wold, S., (1976) Pattern recognition by means of disjoint principal components models, Pattern Recognition 8, 127–139

    Article  Google Scholar 

  28. Martens, H., Naes, T., (1989) Multivariate Calibration, Wiley, London

    Google Scholar 

  29. Kleinbaum, D., Kupper, L., Muller, K., (1988) Applied Regression Analysis and Other Multivariate Methods, 2nd ed.. Pws-Kent, Boston

    Google Scholar 

  30. De Noord, O.E., (1994) Multivariate calibration standardization, Chemometr. Intell. Lab. Syst. 25, 85–97

    Article  Google Scholar 

  31. Anderson, N.L., Hofmann, J.P., Gemmell, A., Taylor, J., (1984) Global approaches to quantitative analysis of gene-expression patterns observed by use of two-dimensional gel electrophoresis, Clin Chem. 30, 2031–2036

    PubMed  CAS  Google Scholar 

  32. Tarroux, P., Vincens, P., Rabilloud, T., (1987) HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part V: Data analysis, Electrophoresis 8, 187–199

    Article  CAS  Google Scholar 

  33. Couto, M.M.B., Vogels, J.T.W.E., Hofstra, H., Husiintveld, J.H.J., Vandervossen, J.M.B.M., (1995) Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified RDNA in taxonomy, 2 Identification techniques for food-borne yeasts, J. Applied Bacteriology 79(5), 525–535

    Article  CAS  Google Scholar 

  34. Johansson, M.L., Quednau, M., Ahrne, S., Molin, G., (1995) Classification of lactobacillus-plantarum by restriction-endonuclease analysis of total chromosomal DNA using conventional agarose-gel electrophoresis, International J. of Systematic Bacteriology 45(4), 670–675

    Article  CAS  Google Scholar 

  35. Boon, N., De Windt, W., Verstraete, W., Top, E.M., (2002) Evaluation o f nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants, FEMS Microbiology Ecology 39(2), 101–112

    PubMed  CAS  Google Scholar 

  36. Gadea, I., Ayala, G., Diago, M.T., Cunat, A., Garcia de Lomas J., (2000) Immunological diagnosis of human hydatid cyst relapse: utility of the enzyme-linked immunoelectrotransfer blot and discriminant analysis, Clinical and Diagnostic Laboratory Immunology 7(4), 549–552

    PubMed  CAS  Google Scholar 

  37. Gadea, I., Ayala, G., Diago, M.T., Cunat, A., Garcia de Lomas, J., (1999) Immunological diagnosis of human cystic echinococcosis: utility of discriminant analysis applied to the enzyme-linked mmunoelectrotransfer blot, Clinical and Diagnostic Laboratory Immunology 6(4), 504–508

    PubMed  CAS  Google Scholar 

  38. Kovarova, H., Hajduch, M., Korinkova, G., Halada, P., Krupickova, S., Gouldsworthy, A., Zhelev, N., Strnad, M., (2000) Proteomics approach in classifying the biochemical basis of the anticancer activity of the new olomoucine-derived synthetic cyclin-dependent kinase inhibitor, bohemine, Electrophoresis 21, 3757–3764

    Article  PubMed  CAS  Google Scholar 

  39. Kovarova, H., Radzioch, D., Hajduch, M., Sirova, M., Blaha, V., Macela, A., Stulik, J., Hernychova, L., (1998) Natural resistance to intracellular parasites: a study by two-dimensional gel electrophoresis coupled with multivariate analysis, Electrophoresis 19(8–9), 1325–1331

    Article  PubMed  CAS  Google Scholar 

  40. De Moor, B., Marchal, K., Mathys, J., Moreau, Y., (2003) Bioinformatics: organisms from Venus, technology from Jupiter, algorithms from Mars, European Journal of Control 9(2–3), 237–278

    Article  Google Scholar 

  41. Iwadate, Y., Sakaida, T., Hiwasa, T., Nagai, Y., Ishikura, H., Takiguchi, M., Yamaura, A., (2004) Molecular classification and survival prediction in human gliomas based on proteome analysis, Cancer Research 64(7), 2496–2501

    Article  PubMed  CAS  Google Scholar 

  42. Amin, R.A., Vickers, A.E., Sistare, F., Thompson, K.L., Roman, R.J., Lawton, M., Kramer, J., Hamadeh, H.K., Collins, J., Grissom, S., Bennett, L., Tucker, C.J., Wild, S., Kind, C., Oreffo, V., Davis, J.W., Curtiss, S., Naciff, J.M., Cunningham, M., Tennant, R., Stevens, J., Car, B., Bertram, T.A., Afsharil, C.A., (2004) Identification of putative gene-based markers of renal toxicity, Environmental Health Perspectives 112(4), 465–479

    Article  PubMed  CAS  Google Scholar 

  43. Heijne, W.H.M., Stierum, R.H., Slijper, M., van Bladeren, P.J., van Ommen, B., (2003) Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach, Biochemical Pharmacology 65 (5), 857–875

    Article  PubMed  CAS  Google Scholar 

  44. Anderson, N.L., EsquerBlasco, R., Richardson, F., Foxworthy, P., Eacho, P., (1996) The effects of peroxisome proliferators on protein abundances in mouse liver, Toxicology and Applied Pharmacology 137(1), 75–89

    Article  PubMed  CAS  Google Scholar 

  45. Perrot, F., Hebraud, M., Charlionet, R., Junter, G.A., Jouenne, T., (2001) Cell immobilisation induces changes in the protein response of Escherichia coli K-12 to a cold shock , Electrophoresis 22, 2110–2119

    Article  PubMed  CAS  Google Scholar 

  46. Verhoeckx, K.C.M., Bijlsma, S., de Groene, E.M., Witkamp, R.F., van der Greef, J., Rodenburg, R.J.T., (2004) A combination of proteomics, principal component analysis and transcriptomics is a powerful tool for the identification of biomarkers for macrophage maturation in the U937 cell line, Proteomics 4(4), 1014–1028

    Article  PubMed  CAS  Google Scholar 

  47. Verhoeckx, K.C.M., Bijlsma, S., Jespersen, S., Ramaker, R., Verheij, E.R., Witkamp, R.F., van der Greef, J., Rodenburg, R.J.T., (2004) Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis, International Immunopharmacology 4(12), 1499–1514

    Article  PubMed  CAS  Google Scholar 

  48. Marengo, E., Robotti, E., Cecconi, D., Scarpa, A., Righetti, P.G., (2004) Identification of the regulatory proteins in human pancreatic cancers treated with Trichostatin-A by 2D-PAGE maps and Multivariate Statistical Analysis, Analytical and Bioanalytical Chemistry 379(7–8), 992–1003

    PubMed  CAS  Google Scholar 

  49. Fujii, K., Kondo, T., Yokoo, H., Yamada, T., Matsuno, Y., Iwatsuki, K., Hirohashi, S., (2005) Protein expression pattern distinguishes different lymphoid neoplasms, Proteomics 5, 4274–4286

    Article  PubMed  CAS  Google Scholar 

  50. Dewettinck, K., Dierckx, S., Eichwalder, P., Huyghebaert, A., (1997) Comparison of SDS-PAGE profiles of four Belgian cheeses by multivariate statistics, Lait 77(1), 77–89

    Article  CAS  Google Scholar 

  51. Alika, J.E., AkenOva, M.E., Fatokun, C.A., (1995) Variation among maize (Zea mays L) accessions of Bendel State, Nigeria – numerical analysis of zein protein band patterns, Genetic Resources and Crop Evolution 42(4), 393–399

    Article  Google Scholar 

  52. Magdic, D., Horvat, D., Jurkovic, Z., Sudar, R., Kurtanjek, K., (2002) Chemometric analysis of high molecular mass glutenin subunits and image data of bread crumb structure from Croatian wheat cultivars, Food Technology and Biotechnology 40(4), 331–341

    CAS  Google Scholar 

  53. Jessen, F., Lametsch, R., Bendixen, E., Kjaersgard, I.V.H., Jorgensen, B.M., (2002) Extracting information from two-dimensional electrophoresis gels by partial least squares regression, Proteomics 2, 32–35

    Article  PubMed  CAS  Google Scholar 

  54. Kleno, T.G., Leonardsen, L.R., Kjeldal, H.O., Laursen, S.M., Jensen, O.N., Baunsgaard, D., (2004) Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis, Proteomics 4, 868–880

    Article  PubMed  CAS  Google Scholar 

  55. Kjaersgard, I.V.H., Norrelykke, M.R., Jessen, F., (2006) Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis, Proteomics 6, 1606–1618

    Article  PubMed  Google Scholar 

  56. Gottfries, J., Sjogren, M., Holmberg, B., Rosengren, L., Davidsson, P., Blennow, K., (2004) Proteomics for drug target discovery, Chemometrics and Intelligent Laboratory Systems 73, 47–53

    Article  CAS  Google Scholar 

  57. Karp, N.A., Griffin, J.L., Lilley, K.S., (2005) Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics, Proteomics 5, 81–90

    Article  PubMed  CAS  Google Scholar 

  58. Norden, B., Broberg, P., Lindberg, C., Plymoth A., (2005) Analysis and understanding of high-dimensionality data by means of multivariate data analysis, Chemistry and Biodiversity 2(11), 1487–1494

    Article  PubMed  CAS  Google Scholar 

  59. Malone, J., McGarry, K., Bowermann, C., (2006) Automated trend analysis of proteomics data using an intelligent data mining architecture, Expert Systems with Applications 30, 24–33

    Article  Google Scholar 

  60. Marengo, E., Robotti, E., Gianotti, V., Righetti P.G., (2003) A new approach to the statistical treatment of 2D-Pages in proteomics using fuzzy logic, Annali di Chimica 93(1–2), 105–116

    PubMed  CAS  Google Scholar 

  61. Marengo, E., Robotti, E., Righetti, P.G., Antonucci, F., (2003) A new approach based on fuzzy logic and principal component analysis for the classification of 2D-maps in health and disease: application to lymphomas, Journal of Chromatography A 1004, 13–28

    Article  PubMed  CAS  Google Scholar 

  62. Marengo, E., Robotti, E., Gianotti, V., Righetti, P.G., Domenici, E., Cecconi, D., (2003) A new integrated statistical approach to the diagnostic use of proteomic two-dimensional maps, Electrophoresis 24, 225–236

    Article  PubMed  CAS  Google Scholar 

  63. Marengo, E., Robotti, E., Cecconi, D., Scarpa, A., Righetti, P.G., (2004) Application of fuzzy logic principles to the classification of 2D-PAGE maps belonging to human pancreatic cancers treated with Trichostatin-A, Proceedings of 2004 IEEE International Conference on Fuzzy Systems, Budapest, Hungary, 25–29 July 2004, 1, 359–364

    Google Scholar 

  64. Marengo, E., Robotti, E., Antonucci, F., Cecconi, D., Campostrini, N., Righetti, P.G., (2005) Spot matching in two-dimensional gels: a review of commercial software and of “home-made” approaches, Proteomics 5 , 654–666

    Article  PubMed  CAS  Google Scholar 

  65. Zenkouar, H., Nachit, A., (1997) Images compression using moments method of orthogonal polynomials, Materials Science and Engineering B 49, 211–215

    Article  Google Scholar 

  66. Yin, J., Rodolfo De Pierro, A., Wei, M., (2002) Analysis for the reconstruction of a noisy signal based on orthogonal moments, Applied Mathematics and Computation 132, 249–263

    Article  Google Scholar 

  67. Hu, M.K., (1962) Visual pattern recognition by moment invariants, IRE Transaction on Information Theory 8, 179–187

    Google Scholar 

  68. Teague, M.R., (1980) Image analysis via the general theory of moments, Journal of the Optical Society of America 70, 920–930

    Article  Google Scholar 

  69. Li, B.C., Shen, J., (1991) Fast computation of moment invariants, Pattern Recognition 24, 807–813

    Article  Google Scholar 

  70. Chong, C., Raveebdram, P., Mukundan, R., (2004) Translation and scale invariants of Legendre moments, Pattern Recognition 37 , 119–129

    Article  Google Scholar 

  71. Mukundan, R., Ramakrishnan, K.R., (1995) Fast computation of Legendre and Zernike moments, Pattern Recognition 28, 1433–1442

    Article  Google Scholar 

  72. Zhou, J.D., Shu, H.Z., Luo, L.M., Yu, W.X., (2002) Two new algorithms for efficient computation of Legendre moments, Pattern Recognition 35, 1143–1152

    Article  Google Scholar 

  73. Wee, C., Paramesran, R., Takeda, F., (2004) New computational methods for full and subset Zernike moments, Information Sciences 159, 203–220

    Article  Google Scholar 

  74. Kan, C., Srinath, M.D., (2002) Invariant character recognition with Zernike and orthogonal Fourier-Mellin moments, Pattern Recognition 35, 143–154

    Article  Google Scholar 

  75. Khotanzad, A., Hong, Y.H., (1990) Invariant image recognition by Zernike moments, IEEE Transactions on Pattern Analysis and Machine Intelligence 12, 489–497

    Article  Google Scholar 

  76. Marengo, E., Bobba, M., Robotti, E., Liparota, M.C., (2005) Use of Legendre moments for the fast comparison of 2D-PAGE maps images, Journal of Chromatography A 1096(1–2), 86–91

    Article  PubMed  CAS  Google Scholar 

  77. Marengo, E., Leardi, R., Robotti, E., Righetti, P.G., Antonucci, F., Cecconi, D., (2003) Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics, Journal of Proteome Research 2(4), 351–360

    Article  PubMed  CAS  Google Scholar 

  78. Schultz, J., Gottlieb, D.M., Petersen, M., Nesic, L., Jacobsen, S., Sondergaard, I., (2004) Explorative data analysis of two-dimensional electrophoresis gels, Electrophoresis 25(3), 502–511

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Environmental and Life Sciences, University of Eastern Piedmont, Alessandria, Italy

    Emilio Marengo, Elisa Robotti & Marco Bobba

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  1. Emilio Marengo
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  2. Elisa Robotti
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  3. Marco Bobba
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  1. Biomedical Research Foundation, Academy of Athens, Athens, Greece

    Antonia Vlahou

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Marengo, E., Robotti, E., Bobba, M. (2008). 2D-PAGE Maps Analysis. In: Vlahou, A. (eds) Clinical Proteomics. Methods in Molecular Biology™, vol 428. Humana Press. https://doi.org/10.1007/978-1-59745-117-8_16

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  • DOI: https://doi.org/10.1007/978-1-59745-117-8_16

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-837-9

  • Online ISBN: 978-1-59745-117-8

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