Differential Analysis of 2-D Maps by Pixel-Based Approaches.

Two approaches to the analysis of 2-D maps are available: the first one involves a step of spot detection on each gel image; the second one is based instead on the direct differential analysis of 2-D map images, following a pixel-based procedure. Both approaches strongly depend on the proper alignment of the gel images, but the pixel-based approach allows to solve important drawbacks of the spot-volume procedure, i.e., the problem of missing data and of overlapping spots. However, this approach is quite computationally intensive and requires the use of algorithms able to separate the information (i.e., spot-related information) from the background. Here, the most recent pixel-based approaches are described.

[1]  A. Householder,et al.  Discussion of a set of points in terms of their mutual distances , 1938 .

[2]  Peter Filzmoser,et al.  Partial robust M-regression , 2005 .

[3]  Harald Martens,et al.  Challenges related to analysis of protein spot volumes from two-dimensional gel electrophoresis as revealed by replicate gels. , 2006, Journal of proteome research.

[4]  Beata Walczak,et al.  Baseline reduction in two dimensional gel electrophoresis images , 2005 .

[5]  D. Massart,et al.  Elimination of uninformative variables for multivariate calibration. , 1996, Analytical chemistry.

[6]  I. J. Schoenberg.  Remarks to Maurice Frechet's Article ``Sur La Definition Axiomatique D'Une Classe D'Espace Distances Vectoriellement Applicable Sur L'Espace De Hilbert , 1935 .

[7]  Beata Walczak,et al.  Automatic preprocessing of electrophoretic images , 2009 .

[8]  Knut Conradsen,et al.  Analysis of Two-Dimensional Electrophoretic Gels , 1992 .

[9]  D. Massart.  Chemometrics: A Textbook , 1988 .

[10]  R. Shepard.  The analysis of proximities: Multidimensional scaling with an unknown distance function. II , 1962 .

[11]  B. Walczak,et al.  About kernel latent variable approaches and SVM , 2005 .

[12]  René Henrion,et al.  A new criterion for simple-structure transformations of core arrays in N-way principal components analysis , 1999 .

[13]  J. Kruskal.  Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis , 1964 .

[14]  Barbara Hubbard,et al.  The World According to Wavelets , 1996 .

[15]  Martin Vetterli,et al.  Adaptive wavelet thresholding for image denoising and compression , 2000, IEEE Trans. Image Process..

[16]  R. Henrion.  Body diagonalization of core matrices in three‐way principal components analysis: Theoretical bounds and simulation , 1993 .

[17]  Beata Walczak,et al.  Preprocessing of two‐dimensional gel electrophoresis images , 2004, Proteomics.

[18]  A. Mahadevan-Jansen,et al.  Automated Method for Subtraction of Fluorescence from Biological Raman Spectra , 2003, Applied spectroscopy.

[19]  Emilio Marengo,et al.  A new method of comparing 2D-PAGE maps based on the computation of Zernike moments and multivariate statistical tools , 2008, Analytical and bioanalytical chemistry.

[20]  Bjørn Tore Gjertsen,et al.  Adaptive contrast enhancement of two‐dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment , 2006, Electrophoresis.

[21]  L. A. Stone,et al.  Computer Aided Design of Experiments , 1969 .

[22]  Michael M Skolnick.  Application of morphological transformations to the analysis of two-dimensional electrophoretic gels of biological materials , 1986 .

[23]  H. Martens,et al.  Modified Jack-knife estimation of parameter uncertainty in bilinear modelling by partial least squares regression (PLSR) , 2000 .

[24]  Beata Walczak,et al.  Wavelets in Chemistry , 2001 .

[25]  D. Massart,et al.  The Radial Basis Functions — Partial Least Squares approach as a flexible non-linear regression technique , 1996 .

[26]  Paul Geladi,et al.  Analysis of multi-way (multi-mode) data , 1989 .

[27]  Serge Beucher,et al.  THE WATERSHED TRANSFORMATION APPLIED TO IMAGE SEGMENTATION , 2009 .

[28]  D. Allison,et al.  Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.

[29]  Beata Walczak,et al.  Pixel‐based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2‐D electrophoresis gel images , 2007 .

[30]  K. Kaczmarek,et al.  Feature Based Fuzzy Matching of 2D Gel Electrophoresis Images , 2002, J. Chem. Inf. Comput. Sci..

[31]  J. Gower.  Some distance properties of latent root and vector methods used in multivariate analysis , 1966 .

[32]  D. Massart,et al.  Application of Radial Basis Functions — Partial Least Squares to non-linear pattern recognition problems: diagnosis of process faults , 1996 .

[33]  Kjell Arild Høgda,et al.  Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables , 2006, BMC Bioinformatics.

[34]  David L. Donoho,et al.  De-noising by soft-thresholding , 1995, IEEE Trans. Inf. Theory.

[35]  Desire L. Massart,et al.  Noise suppression and signal compression using the wavelet packet transform , 1997 .

[36]  David Dagan Feng,et al.  Hybrid registration for two-dimensional gel protein images , 2005, APBC.

[37]  P. Eilers.  Parametric time warping. , 2004, Analytical chemistry.

[38]  Stéphane Mallat,et al.  A Theory for Multiresolution Signal Decomposition: The Wavelet Representation , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[39]  Paul H. C. Eilers,et al.  Fast and compact smoothing on large multidimensional grids , 2006, Comput. Stat. Data Anal..

[40]  R. Henrion.  N-WAY PRINCIPAL COMPONENT ANALYSIS : THEORY, ALGORITHMS AND APPLICATIONS , 1994 .

[41]  Harald Martens,et al.  An improved pixel‐based approach for analyzing images in two‐dimensional gel electrophoresis , 2008, Electrophoresis.

[42]  Richard Sinkhorn.  A Relationship Between Arbitrary Positive Matrices and Doubly Stochastic Matrices , 1964 .

[43]  William H. Press,et al.  Numerical Recipes in C, 2nd Edition , 1992 .

[44]  Valentina Gianotti,et al.  A new integrated statistical approach to the diagnostic use of two‐dimensional maps , 2003, Electrophoresis.

[45]  Age K. Smilde,et al.  Three-way analyses problems and prospects , 1992 .

[46]  Beata Walczak,et al.  Avoiding spots detection in analysis of electrophoretic gel images , 2010 .

[47]  Desire L. Massart,et al.  Local modelling with radial basis function networks , 2000 .

[48]  K. Kaczmarek,et al.  Matching 2D Gel Electrophoresis Images , 2003, J. Chem. Inf. Comput. Sci..

[49]  Emilio Marengo,et al.  Use of Legendre moments for the fast comparison of two-dimensional polyacrylamide gel electrophoresis maps images. , 2005, Journal of chromatography. A.

[50]  Emilio Marengo,et al.  New approach based on fuzzy logic and principal component analysis for the classification of two-dimensional maps in health and disease. Application to lymphomas. , 2003, Journal of chromatography. A.

[51]  B. Everitt,et al.  Three-Mode Principal Component Analysis. , 1986 .

[52]  Bjørn K. Alsberg,et al.  Cross model validated feature selection based on gene clusters , 2006 .

[53]  B. Walczak,et al.  Fuzzy warping of chromatograms , 2005 .

[54]  M Daszykowski,et al.  Start-to-end processing of two-dimensional gel electrophoretic images. , 2007, Journal of chromatography. A.

[55]  J. Neefjes,et al.  Electromigration for separations of protein complexes. , 1999, Journal of chromatography. B, Biomedical sciences and applications.

[56]  N. Otsu.  A threshold selection method from gray level histograms , 1979 .

[57]  L. Tucker,et al.  Some mathematical notes on three-mode factor analysis , 1966, Psychometrika.

[58]  Stanley R Sternberg,et al.  Grayscale morphology , 1986 .

[59]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Asa M Wheelock,et al.  Software‐induced variance in two‐dimensional gel electrophoresis image analysis , 2005, Electrophoresis.

[61]  Dag Magne Ulvang,et al.  Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data , 2013, BMC Bioinformatics.

[62]  Johanna Smeyers-Verbeke,et al.  Handbook of Chemometrics and Qualimetrics: Part A , 1997 .

[63]  M. Fréchet.  Sur La Definition Axiomatique D'Une Classe D'Espaces Vectoriels Distancies Applicables Vectoriellement Sur L'Espace de Hilbert , 1935 .

[64]  Beata Walczak,et al.  Comparison of image-transformation methods used in matching 2D gel electrophoresis images , 2003 .

[65]  Riccardo Leardi,et al.  Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics. , 2003, Journal of proteome research.