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Computational Methods for Analysis of Two-Dimensional Gels

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Bioinformatics Methods in Clinical Research

Part of the book series: Methods in Molecular Biology ((MIMB,volume 593))

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Abstract

Two-dimensional gel electrophoresis (2D gels) is an essential quantitative proteomics technique that is frequently used to study differences between samples of clinical relevance. Although considered to have a low throughput, 2D gels can separate thousands of proteins in one gel, making it a good complementary method to MS-based protein quantification. The main drawback of the technique is the tendency of large and hydrophobic proteins such as membrane proteins to precipitate in the isoelectric focusing step. Furthermore, tests using different programs with distinct algorithms for 2D-gel analysis have shown inconsistent ratio values. The aim here is therefore to provide a discussion of algorithms described for the analysis of 2D gels.

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References

  1. Margolis J, Kenrick KG. (1969) Two-dimensional resolution of plasma proteins by combination of polyacrylamide disc and gradient gel electrophoresis. Nature 221:1056–1057.

    Article  PubMed  CAS  Google Scholar 

  2. O’Farrell PH. (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021.

    PubMed  Google Scholar 

  3. Miller I, Crawford J, Gianazza E. (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6:5385–5408.

    Article  PubMed  CAS  Google Scholar 

  4. Unlu M, Morgan ME, Minden JS. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077.

    Article  PubMed  CAS  Google Scholar 

  5. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I. (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3:36–44.

    Article  PubMed  CAS  Google Scholar 

  6. Clark BN, Gutstein HB. (2008) The myth of automated, high-throughput two-dimensional gel analysis. Proteomics 8:1197–1203.

    Article  PubMed  CAS  Google Scholar 

  7. Dowsey AW, Dunn MJ, Yang GZ. (2003) The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3:1567–1596.

    Article  PubMed  CAS  Google Scholar 

  8. Capel M, Redman B, Bourque DP. (1979) Quantitative comparative analysis of complex two-dimensional electropherograms. Anal Biochem 97:210–228.

    Article  PubMed  CAS  Google Scholar 

  9. Garrels JI. (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 

  10. Schumaker MF. (1978) A program which automatically quantitates gel electrophoretic autoradiograms. Anal Biochem 91:375–393.

    Article  PubMed  CAS  Google Scholar 

  11. Bossinger J, Miller MJ, Vo KP, Geiduschek EP, Xuong NH. (1979) Quantitative analysis of two-dimensional electrophoretograms. J Biol Chem 254:7986–7998.

    PubMed  CAS  Google Scholar 

  12. Anderson NL, Taylor J, Scandora AE, Coulter BP, Anderson NG. (1981) The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns. Clin Chem 27:1807–1820.

    PubMed  CAS  Google Scholar 

  13. Fox SH. (1982) Some relatively simple steps toward a computer system for the analysis of two-dimensional gel-electrophoresis autoradiographs. Clin Chem 28:932–934.

    PubMed  CAS  Google Scholar 

  14. Lemkin P, Merril C, Lipkin L, Van Keuren M, Oertel W, Shapiro B, Wade M, Schultz M, Smith E. (1979) Software aids for the analysis of 2D gel electrophoresis images. Comput Biomed Res 12:517–544.

    Article  PubMed  CAS  Google Scholar 

  15. Lipkin LE, Lemkin PF. (1980) Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. Clin Chem 26:1403–1412.

    PubMed  CAS  Google Scholar 

  16. Alexander A, Cullen B, Emigholz K, Norgard MV, Monahan JJ. (1980) A computer program for displaying two-dimensional gel electrophoresis data. Anal Biochem 103:176–183.

    Article  PubMed  CAS  Google Scholar 

  17. Sanchez JC, Appel RD, Golaz O, Pasquali C, Ravier F, Bairoch A, Hochstrasser DF. (1995) Inside SWISS-2DPAGE database. Electrophoresis 16:1131–1151.

    Article  PubMed  CAS  Google Scholar 

  18. Wilkins MR, Hochstrasser DF, Sanchez JC, Bairoch A, Appel RD. (1996) Integrating two-dimensional gel databases using the Melanie II software. Trends Biochem Sci 21:496–497.

    Article  PubMed  CAS  Google Scholar 

  19. Lemkin PF. (1997) Comparing two-dimensional electrophoretic gel images across the Internet. Electrophoresis 18:461–470.

    Article  PubMed  CAS  Google Scholar 

  20. Lutin WA, Kyle CF, Freeman JA. (1978) Quantitation of brain proteins by computer-analyzed two dimensional electrophoresis. In Developments in Biochemistry (Catsimpoolas N, Ed.), Elsevier North-Holland, Amsterdam, pp. 93–106.

    Google Scholar 

  21. Vo KP, Miller MJ, Geiduschek EP, Nielsen C, Olson A, Xuong NH. (1981) Computer analysis of two-dimensional gels. Anal Biochem 112:258–271.

    Article  PubMed  CAS  Google Scholar 

  22. Skolnick MM. (1982) An approach to completely automatic comparison of two-dimensional electrophoresis gels. Clin Chem 28:979–986.

    PubMed  CAS  Google Scholar 

  23. Jansson PA, Grim LB, Elias JG, Bagley EA, Longerg-Holm KK. (1983) Implementation and application of a method to quantitate 2-D gel electrophoresis patterns. Electrophoresis 4:82–91.

    Article  CAS  Google Scholar 

  24. Olson AD, Miller MJ. (1988) Elsie 4: quantitative computer analysis of sets of two-dimensional gel electrophoretograms. Anal Biochem 169:49–70.

    Article  PubMed  CAS  Google Scholar 

  25. Garrels JI. (1989) The QUEST system for quantitative analysis of two-dimensional gels. J Biol Chem 264:5269–5282.

    PubMed  CAS  Google Scholar 

  26. Garrels JI, Farrar JT, Burwell CB. (1984) The QUEST system for computer-analyzed two-dimensional electrophoresis of proteins. In Two-Dimensional Gel Electrophoresis of Proteins (Celis JE, Bravo R, Eds.), Academic Press, Academic Press, pp. 38–90.

    Google Scholar 

  27. Kuick RD, Skolnick MM, Hanash SM, Neel JV. (1991) A two-dimensional electrophoresis-related laboratory information processing system: spot matching. Electrophoresis 12:736–746.

    Article  PubMed  CAS  Google Scholar 

  28. Lemkin PF, Myrick JM, Lakshmanan Y, Shue MJ, Patrick JL, Hornbeck PV, Thornwal GC, Partin AW. (1999) Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel. Electrophoresis 20:3492–3507.

    Article  PubMed  CAS  Google Scholar 

  29. Pleissner KP, Hoffmann F, Kriegel K, Wenk C, Wegner S, Sahlstrom 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 

  30. Lemkin PF, Lester EP. (1989) Database and search techniques for two-dimensional gel protein data: a comparison of paradigms for exploratory data analysis and prospects for biological modeling. Electrophoresis 10:122–140.

    Article  PubMed  CAS  Google Scholar 

  31. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1:377–396.

    Article  PubMed  CAS  Google Scholar 

  32. Young N, Chang Z, Wishart DS. (2004) GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. Bioinformatics 20:976–978.

    Article  PubMed  CAS  Google Scholar 

  33. Morris JS, Clark BN, Gutstein HB. (2008) Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics 24:529–536.

    Article  PubMed  CAS  Google Scholar 

  34. Dowsey AW, Dunn MJ, Yang GZ. (2008) Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline. Bioinformatics 24:950–957.

    Article  PubMed  CAS  Google Scholar 

  35. Tyson JJ, Haralick RH. (1986) Computer analysis of two-dimensional gels by a general image processing system. Electrophoresis 7:107–113.

    Article  CAS  Google Scholar 

  36. Appel RD, Vargas JR, Palagi PM, Walther D, Hochstrasser DF. (1997) Melanie II – a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 18:2735–2748.

    Article  PubMed  CAS  Google Scholar 

  37. Sternberg SR. (1983) Biomedical image processing. Computer 16:22–34.

    Article  Google Scholar 

  38. Sternberg SR. (1986) Grayscale morphology. Comput Vis Graph Image Process 35:333–355.

    Article  Google Scholar 

  39. Eilers PH. (2004) Parametric time warping. Anal Chem 76:404–411.

    Article  PubMed  CAS  Google Scholar 

  40. Kaczmarek K, Walczak B, De Jong S, Vandeginste BG. (2005) Baseline reduction in two dimensional gel electrophoresis images. Acta Chroma 15:82–96.

    CAS  Google Scholar 

  41. Daszykowski M, Stanimirova I, Bodzon-Kulakowska A, Silberring J, Lubec G, Walczak B. (2007) Start-to-end processing of two-dimensional gel electrophoretic images. J Chromatogr A 1158:306–317.

    Article  PubMed  CAS  Google Scholar 

  42. Kaczmarek K, Walczak B, de Jong S, Vandeginste BG. (2004) Preprocessing of two-dimensional gel electrophoresis images. Proteomics 4:2377–2389.

    Article  PubMed  CAS  Google Scholar 

  43. Wiener N. (1949) Extrapolation, Interpolation, and Smoothing of Stationary Time Series, MIT Press, Cambridge, MA

    Google Scholar 

  44. Berth M, Moser FM, Kolbe M, Bernhardt J. (2007) The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol 76:1223–1243.

    Article  PubMed  CAS  Google Scholar 

  45. Conradsen K, Pedersen J. (1992) Analysis of two-dimensional electrophoretic gels. Biometrics 48:1273–1287.

    Article  Google Scholar 

  46. Vincent L, Soille P. (1991) Watersheds in digital spaces: an efficient algorithm based on immersion simulations. Trans Patt Anal Mach Intell 16:583–598.

    Article  Google Scholar 

  47. 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 

  48. Efrat A, Hoffmann F, Kriegel K, Schultz C, Wenk C. (2002) Geometric algorithms for the analysis of 2D-electrophoresis gels. J Comput Biol 9:299–315.

    Article  PubMed  CAS  Google Scholar 

  49. Yan JX, Sanchez JC, Tonella L, Williams KL, Hochstrasser DF. (1999) Studies of quantitative analysis of protein expression in Saccharomyces cerevisiae. Electrophoresis 20:738–742.

    Article  CAS  Google Scholar 

  50. Dutt MJ, Lee KH. (2001) The scaled volume as an image analysis variable for detecting changes in protein expression levels by silver stain. Electrophoresis 22:1627–1632.

    Article  PubMed  CAS  Google Scholar 

  51. Bettens E, Scheunders P, Van Dyck D, Moens L, Van Osta P. (1997) Computer analysis of two-dimensional electrophoresis gels: a new segmentation and modeling algorithm. Electrophoresis 18:792–798.

    Article  PubMed  CAS  Google Scholar 

  52. Rogers M, Graham J, Tonge RP. (2003) Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images. Proteomics 3:887–896.

    Article  PubMed  CAS  Google Scholar 

  53. Lemkin P, Thornwal GC, Evans J. (2005) Comparing 2-D electrophoretic gels across Internet databases. In The Proteomics Protocols Handbook, 5th ed (Walker JM, Ed.), Humana Press, Totowa, NJ.

    Google Scholar 

  54. Gustafsson JS, Blomberg A, Rudemo M. (2002) Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern. Electrophoresis 23:1731–1744.

    Article  PubMed  CAS  Google Scholar 

  55. Goshtasby, A. (1986) Piecewise linear mapping functions for image registration. Patt Recog 19:459–466.

    Article  Google Scholar 

  56. Goshtasby, A. (1987) Piecewise cubic mapping functions for image registration. Patt Recog 20:525–533.

    Article  Google Scholar 

  57. Rohr K, Cathier P, Wörz S. (2003) Elastic registration of electrophoresis images using intensity information and point landmarks. Patt Recog 3:1035–1048.

    Google Scholar 

  58. Bookstein FL. (1989) Principal warps: thin plate splines and the decomposition of deformations. IEEE Trans Patt Anal Mach Intell 11:567–585.

    Article  Google Scholar 

  59. Aittokallio T, Salmi J, Nyman TA, Nevalainen OS. (2005) Geometrical distortions in two-dimensional gels: applicable correction methods. J Chromatogr B Analyt Technol Biomed Life Sci 815:25–37.

    Article  PubMed  CAS  Google Scholar 

  60. Kaczmarek K, Walczak B, de Jong S, Vandeginste BG. (2002) Feature based fuzzy matching of 2D gel electrophoresis images. J Chem Inf Comput Sci 42:1431–1442.

    PubMed  CAS  Google Scholar 

  61. Kaczmarek K, Walczak B, de Jong S, Vandeginste BG. (2003) Matching 2D gel electrophoresis images. J Chem Inf Comput Sci 43:978–986.

    PubMed  CAS  Google Scholar 

  62. Smilansky Z. (2001) Automatic registration for images of two-dimensional protein gels. Electrophoresis 22:1616–1626.

    Article  PubMed  CAS  Google Scholar 

  63. Veeser S, Dunn MJ, Yang GZ. (2001) Multiresolution image registration for two-dimensional gel electrophoresis. Proteomics 1:856–870.

    Article  PubMed  CAS  Google Scholar 

  64. Salmi J, Aittokallio T, Westerholm J, Griese M, Rosengren A, Nyman TA, Lahesmaa R, Nevalainen O. (2002) Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels. Proteomics 2:1504–1515.

    Article  PubMed  CAS  Google Scholar 

  65. Rohr K, Cathier P, Wörz S. (2004) Elastic registration of electrophoresis images using intensity information and point landmarks. Patt Recog 3:1035–1048.

    Article  Google Scholar 

  66. 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 

  67. Toussaint GT. (1980) The relative neighbourhood graph of a finite planar set. Patt Recog 12:261–268.

    Article  Google Scholar 

  68. Gabriel KR, Sokal RR. (1969) A new statistical approach to geographic variation analysis. Syst Zool 18:259–270.

    Article  Google Scholar 

  69. Lankford PM. (1969) Regionalization: theory and alternative algorithms. Geogr Anal 1:196–212.

    Article  Google Scholar 

  70. Delaunay B. (1934) Sur la sphère vide. Izvestia Akademii Nauk SSR, Otdelenie Matematicheskikh i Estestvennykh Nauk 7:793–800.

    Google Scholar 

  71. Besl PJ. (1992) A method for registration of 3-D shapes. IEEE Trans Patt Anal Mach Intell 14:239–256.

    Article  Google Scholar 

  72. Shi G, Jiang T, Zhu W, Liu B, Zhao H. (2007) Alignment of two-dimensional electrophoresis gels. Biochem Biophys Res Commun 357:427–432.

    Article  PubMed  CAS  Google Scholar 

  73. Rogers M, Graham J, Tonge R. (2004) Two-dimensional electrophoresis gel registration using point matching and local image-based refinement. In British Machine Vision Conference, Kingston University,London

    Google Scholar 

  74. Wolfson HJ, Rigoutsos I. (1997) Geometric hashing: an overview. IEEE Comput Sci Eng 4:10–21.

    Article  Google Scholar 

  75. Schwartz J, Sharir M. (1986) Identification of partially obscured objects in two and three dimensions by matching noisy characteristic curves. Int J Robot Res 6:29–44.

    Article  Google Scholar 

  76. Hoffmann F, Kriegel K, Wenk C. (1999) An Applied Point Pattern Matching Problem: Comparing 2D Patterns of Protein Spots, Vol. 93, Elsevier Science Publishers, Amsterdam, pp. 75–88.

    Google Scholar 

  77. Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD. (2004) SWISS-2DPAGE, ten years later. Proteomics 4:2352–2356.

    Article  PubMed  CAS  Google Scholar 

  78. Douglas D, Jean G. (1996) Topological evolution of surfaces. In Proceedings of the Conference on Graphics Interface ’96, Toronto, Ontario, Canada.

    Google Scholar 

  79. Gokcay E, Principe JC. (2002) Information theoretic clustering. IEEE Trans Patt Anal Mach Intell 24:158–171.

    Article  Google Scholar 

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Authors and Affiliations

  1. Bioinformatics, Parque Technológico de Bizkaia, Derio, Spain

    Gorka Lasso

  2. Instituto de Patologia e Imunologia Molecular da Universidad do Porto - IPATIMUP, Porto, Portugal

    Rune Matthiesen

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  1. Gorka Lasso
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  2. Rune Matthiesen
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  1. Inst. Patologia e Imunologia Molecular, Universidade do Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-465, Portugal

    Rune Matthiesen

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Lasso, G., Matthiesen, R. (2010). Computational Methods for Analysis of Two-Dimensional Gels. In: Matthiesen, R. (eds) Bioinformatics Methods in Clinical Research. Methods in Molecular Biology, vol 593. Humana Press. https://doi.org/10.1007/978-1-60327-194-3_12

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  • DOI: https://doi.org/10.1007/978-1-60327-194-3_12

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  • Print ISBN: 978-1-60327-193-6

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