2D-PAGE maps analysis

Methods in Molecular Biology

Volumn 428, Issue , 2007, Pages 291-325

  Marengo, Emilio ^a   Robotti, Elisa ^a   Bobba, Marco ^a  

^a NONE

Author keywords

Classification; Cluster analysis; Fuzzy logic; Image analysis; Moment functions; Multidimensional scaling; Principal component analysis; SIMCA; Spot volume data; Three way PCA

Indexed keywords

PROTEOME;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; DISCRIMINANT ANALYSIS; FUZZY LOGIC; HUMAN; IMAGE PROCESSING; ISOLATION AND PURIFICATION; METHODOLOGY; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DATABASE; PROTEOMICS; REGRESSION ANALYSIS; STATISTICS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

CLUSTER ANALYSIS; DATABASES, PROTEIN; DISCRIMINANT ANALYSIS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FUZZY LOGIC; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LEAST-SQUARES ANALYSIS; MULTIVARIATE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; PRINCIPAL COMPONENT ANALYSIS; PROTEOME; PROTEOMICS; REGRESSION ANALYSIS; SOFTWARE;

EID: 40549086245     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (78)

1. Mahon, P., Dupree, P., (2001) Quantitative and reproducible two-dimensional gel. analysis using Phoretix 2D Full, Electrophoresis 22, 2075-2085
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
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
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
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
6. Panek, J., Vohradsky, J., (1999) Point pattern matching in the analysis of two-dimensional gel. electropherograms, Electrophoresis 20, 3483-3491
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
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
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
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
11. Moritz, B., Meyer, H.E., (2003) Approaches for the quantification of protein concentration ratios, Proteomics 3, 2208-2220
12. Wheelock, A.M., Buckpitt, A.R., (2005) Software-induced variance in two-dimensional gel electrophoresis image analysis, Electrophoresis 26, 4508-4520
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
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
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
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
17. Garreis, J.I., (1979) Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines, J. Biol. Chem. 254, 7961-7977
18. Garreis, J.I., Farrar, J.T., Burwell IV, C.B., (1984) In: Cells, J.E., Bravo, R. (Eds.), Two-dimensional Gel Electrophoresis of Proteins, Academic Ress, Orlando, FA, USA, pp. 38-91
19. Garreis, J.I, (1989) The QUEST system for quantitative analysis of two-dimensional, gels, J. Biol. Chem. 264, 5269-5282
20. Massart, D.L., Vandeginste, B.G.M., Deming, S.M., Michotte, Y., Kaufman, L., (1988) Chemometrics: A Textbook. Amsterdam, Elsevier
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
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 Rincipal Component Analysis and classification methods, Clinica Chimica Acta 345, 55-67
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
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
25. Eisenbeis, R.A. (Ed.), (1972) Discriminant Analysis and Classification Procedures: Theory and Applications. Lexington, USA
26. Klecka, W.R. (Ed.), (1980) Discriminant Analysis. Sage Publications, Beverly Hills, USA
27. Wold, S., (1976) Pattern recognition by means of disjoint principal components models, Pattern Recognition 8, 127-139
28. Martens, H., Naes, T., (1989) Multivariate Calibration, Wiley, London
29. Kleinbaum, D., Kupper, L., Müller, K., (1988) Applied Regression Analysis and Other Multivariate Methods, 2nd ed.. Pws-Kent, Boston
30. De Noord, O.E., (1994) Multivariate calibration standardization, Chemometr. Intell. Lab. Syst. 25, 85-97
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
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
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
34. Johansson, M.L., Quednau, M., Ahme, 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
35. Boon, N., De Windt, W., Verstraete, W., Top, E.M., (2002) Evaluation of 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
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
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
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 olomoucinederived synthetic cyclin-dependent kinase inhibitor, bohemine, Electrophoresis 21, 3757-3764
39. Kovaova, 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
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
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
42. Amin, R.A., Vickers, AE, Sistare, F., Thompson, K.L., Roman, R.J., Lawton, M., Kramer, J., IIamadeh, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
56. Gottfries, J., Sjogren, M., Holmberg, B., Rosengren, L., Davidsson, P., Blennow, K., (2004) Roteomics for drug target discovery, Chemometrics and Intelligent Laboratory Systems 73, 47-53
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
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
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
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
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
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
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, Roceedings of 2004 IEEE International Conference on Fuzzy Systems, Budapest, Hungary, 25-29 July 2004, 1, 359-364
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
65. Zenkouar, H., Nachit, A., (1997) Images compression using moments method of orthogonal polynomials, Materials Science and Engineering B 49, 211-215
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
67. Hu, M.K., (1962) Visual pattern recognition by moment invariants, IRE Transaction on Information Theory 8, 179-187
68. Teague, M.R., (1980) Image analysis via the general theory of moments, Journal of the Optical Society of America 70, 920-930
69. Li, B.C., Shen, J., (1991) Fast computation of moment invariants, Pattern Recognition 24, 807-813
70. Chong, C., Raveebdram, P., Mukundan, R., (2004) Translation and scale invariants of Legendre moments, Pattern Recognition 37, 119-129
71. Mukundan, R., Ramakrishnan, K.R., (1995) Fast computation of Legendre and Zernike moments, Pattern Recognition 28, 1433-1442
72. Zhou, J.D., Shu, H.Z, Luo, L.M., Yu, W.X., (2002) Two new algorithms forefficient computation of Legendre moments, Pattern Recognition 35, 1143-1152
73. Wee, C., Paramesran, R., Takeda, F., (2004) New computational methods for full and subset Zernike moments, Information Sciences 159, 203-220
74. Kan, C., Srinath, M.D., (2002) Invariant character recognition with Zernike and orthogonal Fourier-Mellin moments, Pattern Recognition 35, 143-154
75. Khotanzad, A., Hong, Y.H., (1990) Invariant image recognition by Zernike moments, IEEE Transactions on Pattern Analysis and Machine Intelligence 12, 489-497
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
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
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