The state of the art in the analysis of two-dimensional gel electrophoresis images

Applied Microbiology and Biotechnology

Volumn 76, Issue 6, 2007, Pages 1223-1243

  Berth, Matthias ^a   Moser, Frank Michael ^a   Kolbe, Markus ^a   Bernhardt, Jörg ^a,b  

^a DECODON GmbH   (Germany)

^b UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

2 D gel electrophoresis; Image analysis; Proteome maps; Statistics; Warping

Indexed keywords

GELS; IMAGE ANALYSIS; SOFTWARE ENGINEERING; STATISTICAL METHODS;

2-D GEL ELECTROPHORESIS; PROTEOME MAPS; WARPING;

ELECTROPHORESIS;

PROTEOME;

DNA; ELECTROKINESIS; GEL; HARDWARE; IMAGE ANALYSIS; IMAGE PROCESSING; PROTEOMICS; SOFTWARE; TWO-DIMENSIONAL MODELING;

COMPUTER PROGRAM; DNA DETERMINATION; DNA MICROARRAY; GENE EXPRESSION; GENETIC ANALYSIS; HYPOTHESIS; IMAGE ANALYSIS; IMAGE PROCESSING; INFORMATION PROCESSING; PROTEIN ANALYSIS; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; SHORT SURVEY; STAINING; STATISTICAL ANALYSIS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION PROFILING; IMAGE PROCESSING, COMPUTER-ASSISTED;

EID: 34648834050     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-007-1128-0     Document Type: Short Survey

References (85)

1. Aittokallio T, Salmi J, Nyman TA, Nevalainen OS (2005) Geometrical distortions in two-dimensional gels: applicable correction method. J Chromatogr B 815:25-37
2. Alban A, Davis SO, Bjorkesten L, Andersson C et al (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
3. Alter O, Brown PO, Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97:10101-10106
4. Amemiya Y, Miyahara J (1988) Imaging plate illuminates many fields. Nature 336(6194):89-90
5. 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
6. Appel R, Hochstrasser D, Roch C, Funk M, Muller AF, Pellegrini C (1988) Automatic classification of two-dimensional gel electrophoresis pictures by heuristic clustering analysis: a step toward machine learning. Electrophoresis 9(3):136-42
7. Appel RD, Hochstrasser DF, Funk M, Vargas JR, Pellegrini C, Muller AF, Scherrer JR (1991) The MELANIE project: from a biopsy to automatic protein map interpretation by computer. Electrophoresis 12:722-735
8. Appel RD, Vargas JR, Palagi PM, Walther D et al (1997) Melanie II-a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 18:2735-2748
9. Bandow JE, Baker JD, Berth M, Painter C, Sepulveda OJ, Clark KA, Kilty I, VanBogelen RA (2007) New image analysis workflow for 2D gels enables large-scale 2D gel-based proteomics studies-example: COPD biomarker discovery study (in press)
10. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57(1):289-300
11. Bernhardt J, Buttner K, Scharf C, Hecker M (1999) Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis 20(11):2225-2240
12. Bernhardt J, Weibezahn J, Scharf C, Hecker M (2003) Bacillus subtilis. during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis. Genome Res 13(2):224-237
13. Bossinger J, Miller MJ, Vo KP, Geiduschek EP, Xuong NH (1979) Quantitative analysis of two-dimensional electrophoretograms. J Biol Chem 254:7986-7998
14. Campostrini N, Areces LB, Rappsilber J, Pietrogrande MC, Dondi F, Pastorino F, Ponzoni M, Righetti PG (2005) Spot overlapping in two-dimensional maps: a serious problem ignored for much too long. Proteomics 5(9):2385-2395 (Jun)
15. Conover WJ (2001) Practical nonparametric statistics, 3rd edn. Wiley, New York
16. Corthals GL, Wasinger VC, Hochstrasser DF, Sanchez JC (2000) The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21(6):1104-1115
17. Deerwester S, Dumais S, Furnas GW, Landauer TK, Harshman R (1990) Indexing by latent semantic analysis. J Soc Inf Sci 41(6):391-407
18. Dowsey AW, Dunn MJ, Yang GZ (2003) The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3(8):1567-1596
19. Dowsey AW, English J, Pennington K, Cotter D, Stuehler K, Marcus K, Meyer HE, Dunn MJ, Yang GZ (2006) Examination of 2-DE in the human proteome organisation brain proteome project pilot studies with the new RAIN gel matching technique. Proteomics 6(18):5030-5047
20. Dukan S, Nyström T (1999) Oxidative stress defense and deterioration of growth-arrested Escherichia coli cells. J Biol Chem 274:26027-26032
21. Eravci M, Fuxius S, Broedel O, Weist S, Eravci S, Mansmann U, Schluter H, Tiemann J, Baumgartner A (2007) Improved comparative proteome analysis based on two-dimensional gel electrophoresis. Proteomics 7(4):513-523
22. Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam le T, Buttner K, Buurman G, Scharf C, Venz S, Volker U, Hecker M (2004) A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4(10):2849-2876
23. Eymann C, Becher D, Bernhardt J, Gronau K, Klutzny A, Hecker M (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics (in press)
24. Fodor IK, Nelson DO, Alegria-Hartman M, Robbins K, Langlois RG, Turteltaub KW, Corzett TH, McCutchen-Maloney SL (2005) Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder. Bioinformatics 21(19):3733-3740
25. Garrels JJ (1989) The QUEST system for quantitative analysis of two-dimensional gels. J Biol Chem 264(9):5269-5282
26. GE Healthcare (2007) DeCyder™ 2-D differential analysis software, user manual. Available from www.gelifesciences.com
27. 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
28. Haas G, Karaali G, Ebermayer K, Metzger WG, Lamer S, Zimny-Arndt U, Diescher S, Goebel UB, Vogt K, Roznowski AB, Wiedenmann BJ, Meyer TF, Aebischer T, Jungblut PR (2002) Immunoproteomics of Helicobacter pylori infection and relation to gastric disease. Proteomics 2(3):313-324
29. Hochgräfe F, Mostertz J, Albrecht D, Hecker M (2005) Fluorescence thiol modification assay: oxidatively modified proteins in Bacillus subtilis. Mol Microbiol 58(2):409-425
30. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci U S A 97:8409-8414
31. Höper D, Bernhardt J, Hecker M (2006) Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach. Proteomics 6(5):1550-1562
32. Horgan G, Creasey A, Fenton B (1992) Superimposing two-dimensional gels to study genetic variation in malaria parasites. Electrophoresis 13(11):871-875
33. Hunt SM, Thomas MR, Sebastian LT, Pedersen SK, Harcourt RL, Sloane AJ, Wilkins MR (2005) Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J Proteome Res 4(3):809-819
34. Johnston RF, Pickett SC, Barker DL (1990) Autoradiography using storage phosphor technology. Electrophoresis 11(5):355-360
35. Karp NA, Lilley KS (2005) Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes. Proteomics 5(12):3105-3115
36. Karp NA, Kreil DP, Lilley KS (2004) Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics 4(5):1421-32
37. Karp NA, Spencer M, Lindsay H, O'Dell K, Lilley KS (2005) Impact of replicate types on proteomic expression analysis. J Proteome Res 4(5):1867-1871
38. Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis in mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26:231-243
39. Klose J, Kobalz U (1995) Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16:1034-1059
40. Kock H, Gerth U, Hecker M (2004) The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis. J Bacteriol 186(17):5856-5864
41. Kreil DP, Karp NA, Lilley KS (2004) DNA microarray normalization methods can remove bias from differential protein expression calls in 2-D difference gel electrophoresis. Bioinformatics 20(13):2026-2034
42. Leichert LI, Jakob U (2004) Protein thiol modifications visualized in vivo. PLoS Biol 2(11):e333
43. Lemkin PF (1989) GELLAB-II: a workstation based 2D electrophoresis gel analysis system. In: Endler T, Hanash S (eds) Proceedings of two-dimensional electrophoresis. VCH Press, Weinheim, pp 53-57
44. Lemkin PF, Lipkin LE (1981a) GELLAB: a computer system for 2D gel electrophoresis analysis I. Segmentation of spots and system preliminaries. Comput Biomed Res 14:272-297
45. Lemkin PF, Lipkin LE (1981b) GELLAB: a computer system for 2D gel electrophoresis analysis. II. Pairing spots. Comput Biomed Res 14:355-380
46. Lemkin PF, Lipkin LE (1981c) GELLAB: a computer system for twodimensional gel electrophoresis analysis. III. Multiple two-dimensional gel analysis. Comput Biomed Res 14:407-446
47. Luhn S, Berth M, Hecker M, Bernhardt J (2003) Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics 3(7):1117-1127
48. Manly KF, Nettleton D, Hwang JTG (2004) Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res 14:997-1001
49. Meunier B, Dumas E, Piec I, Bechet D, Hebraud M, Hocquette JF (2007) Assessment of hierarchical clustering methodologies for proteomic data mining. J Proteome Res 6:358-366
50. Miura K (2003) Imaging technologies for the detection of multiple stains in proteomics. Proteomics 3:1097-1108
51. Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA (2003) Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3(10):1912-1919
52. Mostertz J, Hecker M (2003) Patterns of protein carbonylation following oxidative stressin wild-type and sigB Bacillus subtilis cells. Mol Gen Genomics 269:640-648
53. Nishihara JC, Champion KM (2002) Quantitative evaluation of proteins in one- and two-dimensional polyacrylamide gels using a fluorescent stain. Electrophoresis 23:2203-2215
54. O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007-4021
55. Olson AD, Miller MJ (1988) Elsie 4: quantitative computer analysis of sets of two-dimensional gel electrophoretograms. Anal Biochem 169:49-70
56. Patton WF (2002) Detection technologies in proteome analysis. J Chromatogr B 771:3-31
57. Patton WF, Beechem JM (2002) Rainbow's end: the quest for multiplexed fluorescence quantitative analysis in proteomics. Curr Opin Chem Biol 6(1):63-69
58. Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A (2005) False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21(13):3017-3024
59. Pietrogrande MC, Marchetti N, Dondi F, Righetti PG (2002) Spot overlapping in two-dimensional polyacrylamide gel electrophoresis separations: a statistical study of complex protein maps. Electrophoresis 23:283-291
60. Pounds SB (2006) Estimation and control of multiple testing error rates for microarray studies. Brief Bioinform 7(1):25-36
61. Roegener J, Lutter P, Reinhardt R, Bluggel M, Meyer HE, Anselmetti D (2003) Ultrasensitive detection of unstained proteins in acrylamide gels by native UV fluorescence. Anal Chem 75(1):157-159
62. Rowlands DG, Flook A, Payne PI, van Hoff A et al (1988) GESA-a two-dimensional processing system using knowledge base techniques. Electrophoresis 9:820-830
63. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34(2):374-378
64. Shlens J (2005) A tutorial on principal component analysis. Systems Neurobiology Laboratory, Salk Insitute for Biological Studies La Jolla. http://www.cs.cmu.edu/∼elaw/papers/pca.pdf (accessed April 2007)
65. Skolnick MM (1986) Application of morphological transformations to the analysis of two-dimensional electrophoresis gels of biological materials. Comput Vis Graph Image Process 35:306-322
66. Skolnick MM, Sternberg SR, Neel JV (1982) Computer programs for adapting two-dimensional gels to the study of mutation. Clin Chem 28(4 Pt 2):969-978
67. Smilansky Z (2001) Automatic registration for images of two-dimensional protein gels. Electrophoresis 22:1616-1626
68. Steinberg TH, Agnew BJ, Gee KR, Leung WY, Goodman T, Schulenberg B, Hendrickson J, Beechem JM, Haugland RP, Patton WF (2003) Global quantitative phosphoprotein analysis using multiplexed proteomics technology. Proteomics 3(7):1128-1144
69. Tam le T, Antelmann H, Eymann C, Albrecht D, Bernhardt J, Hecker M (2006) Proteome signatures for stress and starvation in Bacillus subtilis as revealed by a 2-D gel image color coding approach. Proteomics 6(16):4565-4585
70. Tan HY, Ng TW, Liew OW (2007) Effects of light spectrum in flatbed scanner densitometry of stained polyacrylamide gels. BioTechniques 42:474-478
71. Tarroux P, Vincens P, Meyer JA (1989) Processing of two-dimensional gel electrophoresis data. In: Endler T, Hanash S (eds) Proceedings of two-dimensional electrophoresis. VCH Press, Weinheim, pp 68-71
72. Tokarski C, Cren-Olivé C, Fillet M, Rolando C (2006) High-sensitivity staining of proteins for one- and two-dimensional gel electrophoresis using post migration covalent staining with a ruthenium fluorophore. Electrophoresis 27(7):1407-1416
73. Turk M, Pentland A (1991) Face recognition using eigenfaces. Proc. IEEE Conference on Computer Vision and Pattern Recognition 586-591
74. Tyson JJ, Haralick RH (1986) Computer analysis of two-dimensional gels by a general image processing system. Electrophoresis 7:107-112
75. Unlü M, Morgan ME, Minden JS (1998) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18(11):2071-2077
76. Vincens P, Tarroux P (1987) HERMeS; a second generation approach to the automatic analysis of two-dimensional electrophoresis gels Part III: spot list matching. Electrophoresis 8:100-107
77. Vo KP, Miller MJ, Geiduschek EP, Nielsen C, Olson A, Xuong NH (1981) Computer analysis of two-dimensional gels. Anal Biochem 112:258-271
78. Voigt B, Schweder T, Sibbald MJ, Albrecht D, Ehrenreich A, Bernhardt J, Feesche J, Maurer KH, Gottschalk G, van Dijl JM, Hecker M (2006) The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions. Proteomics 6(1):268-281
79. 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
80. Wall ME, Rechtsteiner A, Rocha LM (2003) Singular value decomposition and principal component analysis. In: Berrar DP, Dubitzky W, Granzow M (eds) A practical approach to microarray data analysis. Kluwer, Norwell, pp 91-109 (MA. LANL LA-UR-02-4001, http://public.lanl.gov/mewall/kluwer2002.html, accessed April 2007)
81. Weisstein EW (2007a) Bonferroni correction. From MathWorld - a Wolfram web resource. http://mathworld.wolfram.com/BonferroniCorrection.html, accessed April 2007
82. Weisstein EW (2007b) ANOVA. From MathWorld - a Wolfram web resource. http://mathworld.wolfram.com/ANOVA.html, accessed April 2007
83. Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Görg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ (2006) Guidelines for the next 10 years of proteomics. Proteomics 6(1):4-8
84. Wolff S, Otto A, Albrecht D, Zeng JS, Buttner K, Gluckmann M, Hecker M, Becher D (2006) Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study. Mol Cell Proteomics 5(7):1183-1192
85. Wolff S, Antelmann H, Albrecht D, Becher D, Bernhardt J, Bron S, Buttner K, van Dijl JM, Eymann C, Otto A, Tam LT, Hecker M (2007) Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J Chromatogr B Analyt Technol Biomed Life Sci 849(1-2):129-140