Abstract
The comparison of 2-D maps is not trivial, the main difficulties being the high complexity of the sample and the large experimental variability characterizing 2-D gel electrophoresis. The comparison of maps from control and treated samples is usually performed by specific software, providing the so-called spot volume dataset where each spot of a specific map is matched to its analogous in other maps, and they are described by their optical density, which is supposed to be related to the underlying protein amount. Here, a different approach is presented, based on the direct comparison of 2-D map images: each map is decomposed in terms of moment functions, successively applying the multivariate tools usually adopted in image analysis problems. The moments calculated are then treated with multivariate classification techniques. Here, two types of moment functions are presented (Legendre and Zernike moments), while linear discriminant analysis and partial least squares discriminant analysis are exploited as classification tools to provide the classification of the samples. The procedure is applied to a sample dataset to prove its effectiveness.
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References
Kossowska B, Dudka I, Bugla-Ploskonska G, Szymanska-Chabowska A, Doroszkiewicz W, Gancarz R, Andrzejak R, Antonowicz-Juchniewicz J (2010) Proteomic analysis of serum of workers occupationally exposed to arsenic, cadmium, and lead for biomarker research: a preliminary study. Sci Total Environ 408(22):5317–5324
Rodriguez-Pineiro AM, Blanco-Prieto S, Sanchez-Otero N, Rodriguez-Berrocal FJ, Paez de la Cadena M (2010) On the identification of biomarkers for non-small cell lung cancer in serum and pleural effusion. J Proteomics 73(8):1511–1522
Poulsen NA, Andersen V, Moller JC, Moller HS, Jessen F, Purup S, Larsen LB (2012) Comparative analysis of inflamed and non-inflamed colon biopsies reveals strong proteomic inflammation profile in patients with ulcerative colitis. BMC Gastroenterol 12:N76
Bouwman FG, de Roos B, Rubio-Aliaga I, Crosley LK, Duthie SJ, Mayer C, Horgan G, Polley AC, Heim C, Coort SLM, Evelo CT, Mulholland F, Johnson IT, Elliott RM, Daniel H, Mariman ECM (2011) 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting. BMC Med Genomics 4:N24
Ocak S, Friedman DB, Chen H, Ausborn JA, Hassanein M, Detry B, Weynand B, Aboubakar F, Pilette C, Sibille Y, Massion PP (2014) Discovery of new membrane-associated proteins overexpressed in small-cell lung cancer. J Thorac Oncol 9(3):324–336
Fernando H, Wiktorowicz JE, Soman KV, Kaphalia BS, Khan MF, Ansari GAS (2013) Liver proteomics in progressive alcoholic steatosis. Toxicol Appl Pharmacol 266(3):470–480
O’Dwyer D, Ralton LD, O’Shea A, Murray GI (2011) The proteomics of colorectal cancer: identification of a protein signature associated with prognosis. Plos One 6(11):e27718
Pitarch A, Jimenez A, Nombela C, Gil C (2006) Decoding serological response to Candida cell wall immunome into novel diagnostic, prognostic, and therapeutic candidates for systemic candidiasis by proteomic and bioinformatic analyses. Mol Cell Proteomics 5(1):79–96
Marengo E, Robotti E, Bobba M, Milli A, Campostrini N, Righetti SC, Cecconi D, Righetti PG (2008) Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study. Anal Bioanal Chem 390:1327–1342
Sofiadis A, Becker S, Hellman U, Hultin-Rosenberg L, Dinets A, Hulchiy M, Zedenius J, Wallin G, Foukakis T, Hoog A, Auer G, Lehtio J, Larsson C (2012) Proteomic profiling of follicular and papillary thyroid tumors. Eur J Endocrinol 166(4):657–667
Marengo E, Robotti E, Righetti PG, Campostrini N, Pascali J, Ponzoni M, Hamdan M, Astner H (2004) Study of proteomic changes associated with healthy and tumoral murine samples in neuroblastoma by principal component analysis and classification methods. Clin Chim Acta 345:55–67
Marengo E, Robotti E, Bobba M, Liparota MC, Rustichelli C, Zamò A, Chilosi M, Righetti PG (2006) Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis. Electrophoresis 27:484–494
Haas B, Serchi T, Wagner DR, Gilson G, Planchon S, Renaut J, Hoffmann L, Bohn T, Devaux Y (2011) Proteomic analysis of plasma samples from patients with acute myocardial infarction identifies haptoglobin as a potential prognostic biomarker. J Proteomics 75(1):229–236
Marengo E, Robotti E, Cecconi D, Hamdan M, Scarpa A, Righetti PG (2004) Identification of the regulatory proteins in human pancreatic cancers treated with Trichostatin A by 2D-PAGE maps and multivariate statistical analysis. Anal Bioanal Chem 379:992–1003
Schmid HR, Schmitter D, Blum O, Miller M, Vonderschmitt D (1995) Lung-tumor cells – a multivariate approach to cell classification using 2-dimensional protein pattern. Electrophoresis 16:1961–1968
Maurer MH (2006) Software analysis of two-dimensional electrophoretic gels in proteomic experiments. Curr Bioinform 1:255–262
Mahon P, Dupree P (2001) Quantitative and reproducible two-dimensional gel analysis using Phoretix 2D Full. Electrophoresis 22:2075–2085
Appel RD, Vargas JR, Palagi PM et al (1997) Melanie II—a third-generation software package for analysis of two- dimensional electrophoresis images: II. Algorithms. Electrophoresis 18:2735–2748
Jensen K, Kesmir C, Sondergaard I (1996) From image processing to classification.4. Classification of electrophoretic patterns by neural networks and statistical methods enable quality assessment of wheat varieties for breadmaking. Electrophoresis 17:694–698
Grus FH, Augustin AJ (2000) Protein analysis methods in diagnosis of sicca syndrome. Ophthalmologe 97:54–61
Swets D, Weng J (1996) Using discriminant eigenfeatures for image retrieval. IEEE Trans Pattern Anal Mach Intell 18:831–836
Marengo E, Bobba M, Liparota MC, Robotti E, Righetti PG (2005) Use of Legendre moments for the fast comparison of two-dimensional polyacrylamide gel electrophoresis maps images. J Chromatogr A 1096:86–91
Teague MR (1980) Image analysis via the general theory of moments. J Opt Soc Am 70:920–930
Zernike F (1934) Beugungstheorie des schneidenver-fahrens und seiner verbesserten form, der phasenkontrastmethode. Physica 1:689–704
Marengo E, Robotti E, Bobba M, Demartini M, Righetti PG (2008) A new method of comparing 2D-PAGE maps based on the computation of Zernike moments and multivariate statistical tools. Anal Bioanal Chem 391:1163–1173
Marengo E, Cocchi M, Demartini M, Robotti E, Bobba M, Righetti PG (2011) Investigation of the applicability of Zernike moments to the classification of SDS 2D-PAGE maps. Anal Bioanal Chem 400:1419–1431
Wee C, Paramesran R, Takeda F (2004) New computational methods for full and subset Zernike moments. Inform Sci 159:203–220
Kan C, Srinath MD (2002) Invariant character recognition with Zernike and orthogonal Fourier-Mellin moments. Pattern Recogn 35:143–154
Zenkouar H, Nachit A (1997) Images compression using moments method of orthogonal polynomials. Mat Sci Eng B Solid 49:211–215
Yin J, De Pierro RA, Wei M (2002) Analysis for the reconstruction of a noisy signal based on orthogonal moments. Appl Math Comput 132:249–263
Hu MK (1962) Visual pattern recognition by moment invariants. IRE Trans Inf Theor 8:179–187
Khotanzad A, Hong YH (1990) Invariant image recognition by Zernike moments. IEEE Trans Pattern Anal Mach Intell 12:489–497
Li BC, Shen J (1991) Fast computation of moment invariants. Pattern Recogn 24:807–813
Chong C, Raveendran P, Mukundan R (2004) Translation and scale invariants of Legendre moments. Pattern Recogn 37:119–129
Mukundan R, Ramakrishnan KR (1995) Computation of Legendre and Zernike moments. Pattern Recogn 28:1433–1442
Zhou JD, Shu HZ, Luo LM, Yu WX (2002) Two new algorithms for efficient computation of Legendre moments. Pattern Recogn 35:1143–1152
Mukundan R, Ramakrishnan KR (1998) Moment function in image analysis. World Scientific, Singapore
Chong CW, Raveendran P, Mukundan R (2003) A comparative analysis of algorithms for fast computation of Zernike moments. Pattern Recogn 36:731–742
Belkasim SO, Shridhar M, Ahmadi M (1991) Pattern recognition with moment invariants—a comparative study and new results. Pattern Recogn 24:1117–1138
Teh CH, Chin RT (1988) On image analysis by the method of moments. IEEE Trans Pattern Anal Mach Intell 10:496–513
Massart DL, Vandeginste BGM, Deming SM, Michotte Y, Kaufman L (1988) Chemometrics: a textbook. Elsevier, Amsterdam
Vandeginste BGM, Massart DL, Buydens LMC, De Yong S, Lewi PJ, Smeyers-Verbeke J (1988) Handbook of chemometrics and qualimetrics: part B. Elsevier, Amsterdam
Frank IE, Lanteri S (1989) Classification models: discriminant analysis, SIMCA, CART. Chemometr Intell Lab Syst 5:247–256
Martens H, Naes T (1989) Multivariate calibration. Wiley, London
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Marengo, E., Robotti, E., Demartini, M. (2016). The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps. In: Marengo, E., Robotti, E. (eds) 2-D PAGE Map Analysis. Methods in Molecular Biology, vol 1384. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3255-9_15
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DOI: https://doi.org/10.1007/978-1-4939-3255-9_15
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