Two-Dimensional Gel Electrophoresis Image Analysis.
2D-PAGE
Image analysis
Image preprocessing
Spot detection and quantification
Spot matching
Warping
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
8
7
2021
pubmed:
9
7
2021
medline:
12
1
2022
Statut:
ppublish
Résumé
Gel-based proteomics is still quite widespread due to its high-resolution power; the experimental approach is based on differential analysis, where groups of samples (e.g., control vs diseased) are compared to identify panels of potential biomarkers. However, the reliability of the result of the differential analysis is deeply influenced by 2D-PAGE maps image analysis procedures. The analysis of 2D-PAGE images consists of several steps, such as image preprocessing, spot detection and quantitation, image warping and alignment, spot matching. Several approaches are present in literature, and classical or last-generation commercial software packages exploit different algorithms for each step of the analysis. Here, the most widespread approaches and a comparison of the different strategies are presented.
Identifiants
pubmed: 34236652
doi: 10.1007/978-1-0716-1641-3_1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
3-13Références
Sheenan D, Tyther R (eds) (2009) Two-dimensional electrophoresis protocols. Methods in molecular biology, vol 519. Humana Press, Totowa, NJ
Marengo E, Robotti E, Bobba M (2008) 2DPAGE maps analysis. In: Vlahou A (ed) Clinical proteomics: methods and protocols. Methods in molecular biology, vol 428. Humana Press, Totowa, NJ, pp 291–325
Marengo E, Robotti E (eds) (2016) 2D-PAGE maps analysis. Methods in molecular biology, vol 1384. Humana Press, Totowa, NJ
Rye M, Fargestad EM (2012) Preprocessing of electrophoretic images in 2-DE analysis. Chemom Intell Lab Syst 117:70–79
Moller B, Posch S (2009) Robust features for 2-DE gel image registration. Electrophoresis 30:4137–4148
pubmed: 19960478
Srinark T, Kambhamettu C (2008) An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels. Electrophoresis 29:706–715
pubmed: 18203251
Liu YS, Chen SY, Liu RS, Duh DJ, Chao YT, Tsai YC, Hsieh JS (2009) Spot detection for a 2-DE gel image using a slice tree with confidence evaluation. Math Comput Model 50:1–14
Cutler P, Heald G, White IR, Ruan J (2003) A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection. Proteomics 3:392–401
pubmed: 12687607
Kazhiyur-Mannar R, Smiraglia DJ, Plass C, Wenger R (2006) Contour area filtering of two-dimensional electrophoresis images. Med Image Anal 10:353–365
pubmed: 16531098
Wu Y, Lemkin PF, Upton K (1993) A fast spot segmentation algorithm for two-dimensional gel electrophoresis analysis. Electrophoresis 14:1351–1356
pubmed: 8137801
Bettens E, Scheunders P, VanDyck D, Moens L, VanOsta P (1997) Computer analysis of two-dimensional electrophoresis gels: a new segmentation and modeling algorithm. Electrophoresis 18:792–798
pubmed: 9194609
Tsakanikas P, Manolakos ES (2011) Protein spot detection and quantification in 2-DE gel images using machine-learning methods. Proteomics 11:2038–2050
pubmed: 21500344
Langella O, Zivy M (2008) A method based on bead flows for spot detection on 2-D gel images. Proteomics 8:4914–4918
pubmed: 19003871
Veeser S, Dunn MJ, Yang GZ (2001) Multiresolution image registration for two-dimensional gel electrophoresis. Proteomics 1:856–870
pubmed: 11503210
Dowsey AW, English J, Pennington K, Cotter D et al (2006) Examination of 2-DE in the Human Proteome Organisation Brain Proteome Project pilot studies with the new RAIN gel matching technique. Proteomics 6:5030–5047
pubmed: 16927431
Dowsey AW, Dunn MJ, Yang GZ (2003) The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3:1567–1596
pubmed: 12923783
Conradsen K, Pedersen J (1992) Analysis of two-dimensional electrophoretic gels. Biometrics 48:1273–1287
Woodward AM, Rowland JJ, Kell DB (2004) Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels. Analyst 129:542–552
pubmed: 15152333
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 3:1117–1127
pubmed: 12872213
Schultz J, Gottlieb DM, Petersen M, Nesic L, Jacobsen S, Sondergaard I (2004) Explorative data analysis of two-dimensional electrophoresis gels. Electrophoresis 25:502–511
pubmed: 14760644
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
pubmed: 12442250
Panek J, Vohradsky J (1999) Point pattern matching in the analysis of two-dimensional gel electropherograms. Electrophoresis 20:3483–3491
pubmed: 10612274
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: 12444741
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
pubmed: 12179995
Smilansky Z (2001) Automatic registration for images of two-dimensional protein gels. Electrophoresis 22:1616–1626
pubmed: 11425217
Sorzano CO, Arganda-Carreras I, Thevenaz P, Beloso A, Morales G, Valdes I, Perez-Garcia C, Castillo C, Garrido E, Unser M (2008) Elastic image registration of 2-D gels for differential and repeatability studies. Proteomics 8:62–65
pubmed: 18050274
Daszykowski M, Faergestad EM, Grove H, Martens H, Walczak B (2009) Matching 2D gel electrophoresis images with Matlab ‘Image Processing Toolbox’. Chemom Intell Lab Syst 96:188–195
Potra FA, Liu X, Seillier-Moiseiwitsch F, Roy A, Hang Y, Marten MR, Raman B, Whisnant C (2006) Protein image alignment via piecewise affine transformations. J Comput Biol 13:614–630
pubmed: 16706715
Rogers M, Graham J (2007) Robust and accurate registration of 2-D electrophoresis gels using point-matching. IEEE Trans Image Process 16:624–635
pubmed: 17357724
Noma A, Pardo A, Cesar RM (2011) Structural matching of 2D electrophoresis gels using deformed graphs. Pattern Recogn Lett 32:3–11
Xin HM, Zhu Y (2009) Multiple information based spot matching method for 2-DE images. Electrophoresis 30:2477–2480
pubmed: 19639568
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 2DPAGE maps and multivariate statistical analysis. Anal Bioanal Chem 379(7–8):992–1003
pubmed: 15257427
Marengo E, Robotti E, Bobba M, Liparota MC, Rustichelli C, Zamo A, Chilosi M, Righetti PG (2006) Multivariate statistical tools applied to the characterisation of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis. Electrophoresis 27(2):484–494
pubmed: 16372308
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(5):1327–1342
pubmed: 18224487
Robotti E, Demartini M, Gosetti F, Calabrese G, Marengo E (2011) Development of a classification and ranking method for the identification of possible biomarkers in two-dimensional gel-electrophoresis based on principal component analysis and variable selection procedures. Mol BioSyst 7(3):677–686
pubmed: 21286649
Negri AS, Robotti E, Prinsi B, Espen L, Marengo E (2011) Proteins involved in biotic and abiotic stress responses as the most significant biomarkers in the ripening of Pinot Noir skins. Funct Integr Genomics 11(2):341–355
pubmed: 21234783
Polati R, Menini M, Robotti E, Millioni R, Marengo E, Novelli E, Balzan S, Cecconi D (2012) Proteomic changes involved in tenderization of bovine Longissimus dorsi muscle during prolonged aging. Food Chem 135(3):2052–2069
pubmed: 22953957
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(1–2):55–67
pubmed: 15193978
Marengo E, Robotti E, Gianotti V, Righetti PG, Cecconi D, Domenici E (2003) A new integrated statistical approach to the diagnostic use of proteomic two-dimensional maps. Electrophoresis 24(1–2):225–236
pubmed: 12652595
Marengo E, Robotti E, Righetti PG, Antonucci F (2003) New approach based on fuzzy logic and principal component analysis for the classification of two-dimensional maps in health and disease: application to lymphomas. J Chromatogr A 1004(1–2):13–28
pubmed: 12929957
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(1–2):86–91
pubmed: 16301071
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(5):1419–1431
pubmed: 21404090
Marengo E, Robotti E, Bobba M, Demartini M, Righetti PG (2008) A new method for comparing 2D-PAGE maps based on the computation of Zernike moments and multivariate statistical tools. Anal Bioanal Chem 391(4):1163–1173
pubmed: 18256813
Carpentier S, Panis B, Swennen R, Lammertyn J (2008) Finding the significant markers: statistical analysis of proteomic data. In: Vlahou A (ed) Clinical proteomics. Methods in molecular biology, vol 428. Humana Press, Totowa, NJ, pp 327–347
Jacobsen S, Grove H, Jensen KN, Sorensen HA, Jessen F, Hollung K, Uhlen AK, Jorgensen BM, Faergestad EM, Sondergaard I (2007) Multivariate analysis of 2-DE protein patterns—practical approaches. Electrophoresis 28:1289–1299
pubmed: 17351893
Faergestad EM, Rye MB, Nhek S, Hollung K, Grove H (2011) The use of chemometrics to normalization for 2-DE and 2-D-DIGE analyse protein patterns from gel electrophoresis. Acta Chromatogr 23:1–40
Grove H, Jorgensen BM, Jessen F, Sondergaard I, Jacobsen S, Hollung K, Indahl U, Faergestad EM (2008) Combination of statistical approaches for analysis of 2-DE data gives complementary results. J Proteome Res 7(12):5119–5124
pubmed: 19367717
Bandow JE, Baker JD, Berth M, Painter C, Sepulveda OJ, Clark KA, Kilty I, VanBogelen RA (2008) Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies—COPD biomarker discovery study. Proteomics 8:3030–3041
pubmed: 18618493
Rye MB, Faergestad EM, Alsberg BK (2008) A new method for assigning common spot boundaries for multiple gels in two dimensional gel electrophoresis. Electrophoresis 29:1359–1368
pubmed: 18348212
Clark BN, Gutstein HB (2008) The myth of automated, high-throughput two-dimensional gel analysis. Proteomics 8:1197–1203
pubmed: 18283661
Morris JS, Clark BN, Wei W, Gutstein HB (2010) Evaluating the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies. J Proteome Res 9:595–604
pubmed: 19919108
pmcid: 2802214
Faergestad EM, Rye M, Walczak B, Gidskehaug L, Wold JP, Grove H, Jia X, Hollung K, Indahl UG, Westad F, van den Berg F, Martens H (2007) Pixel-based analysis of multiple images for the identification of changes: a novel approach applied to unravel proteome patterns [corrected] of 2-D electrophoresis gel images. Proteomics 7:3450–3461
pubmed: 17726676
Rye MB, Faergestad EM, Martens H, Wold JP, Alsberg BK (2008) An improved pixel-based approach for analyzing images in two dimensional gel electrophoresis. Electrophoresis 29:1382–1393
pubmed: 18348214
Van Belle W, Anensen N, Haaland I, Bruserud O, Hogda KA, Gjertsen BT (2006) Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables. BMC Bioinformatics 7:198
pubmed: 16606449
pmcid: 1559651
Daszykowski M, Stanimirova I, BodzonKulakowska A, Silberring J, Lubec G, Walczak B (2007) Start-to-end processing of two dimensional gel electrophoretic images. J Chromatogr A 1158:306–317
pubmed: 17335835
Rogers M, Graham J, Tonge RP (2003) Using statistical image models for objective evaluation of spot detection in two-dimensional gels. Proteomics 3(6):879–886
pubmed: 12833511
Tsakanikas P, Manolakos ES (2009) Improving 2-DE gel image denoising using contourlets. Proteomics 9(15):3877–3888
pubmed: 19670247
Tsakanikas P, Manolakos I (2007) Effective denoising of 2D gel proteomics images using contourlets. In: Image processing, 2007, ICIP 2007. IEEE international conference on 2, 1–22
Marengo E, Robotti E, Antonucci F et al (2005) Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems. Proteomics 5:654–666
pubmed: 15669000
Appel RD, Palagi PM, Walther D et al (1997) Melanie II—a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface. Electrophoresis 18:2724–2734
pubmed: 9504804
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
pubmed: 9504805
Kaczmarek K, Walczak B, deJong S et al (2004) Preprocessing of two-dimensional gel electrophoresis images. Proteomics 4:2377–2389
pubmed: 15274133
Cannistraci CV, Montevecchi FM, Alessio M (2009) Median-modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing. Proteomics 9:4908–4919
pubmed: 19862762
Robotti E, Marengo E, Quasso F (2016) Image pretreatment tools II: normalization techniques for 2-DE and 2-D DIGE. Methods Mol Biol 1384:91–107
pubmed: 26611411
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
pubmed: 10344245
Silva E, O’Gorman M, Becker S, Auer G, Eklund A, Grunewald J, Wheelock AM (2010) In the eye of the beholder: does the master see the SameSpots as the novice? J Proteome Res 9(3):1522–1532
pubmed: 20108985
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
pubmed: 12833512
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
pubmed: 17713763
pmcid: 2279157
Rohr K, Cathier P, Worz S (2004) Elastic registration of electrophoresis images using intensity information and point landmarks. Pattern Recogn 37:1035–1048
Shi G, Jiang T, Zhu W, Liu B, Zhao H (2007) Alignment of two-dimensional electrophoresis gels. Biochem Biophys Res Commun 357:427–432
pubmed: 17434143
Raman B, Cheung A, Marten MR (2002) Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie. Electrophoresis 23:2194–2202
pubmed: 12210223
Lemkin PF (1997) Comparing twodimensional gels across the internet. Electrophoresis 18(3–4):461–470
pubmed: 9150925
Efrat A, Hoffmann F, Kriegel K, Schultz C, Wenk C (2002) Geometric algorithms for the analysis of 2D-electrophoresis gels. J Comput Biol 9(2):299–316
pubmed: 12015883
Bookstein FL (1989) Principal warps: thinplate splines and the decomposition of deformation. IEEE Trans Pattern Anal Mach Intell 11:567–585
Marengo E, Cocchi M, Demartini M, Robotti E, Cecconi D, Calabrese G (2012) GENOCOP algorithm and hierarchical grid transformation for image warping of two dimensional gel electrophoretic maps. Mol BioSyst 8(4):975–984
pubmed: 22301843
Robotti E, Marengo E, Demartini M (2016) GENOCOP algorithm and hierarchical grid transformation for image warping of two-dimensional gel electrophoretic maps. Methods Mol Biol 1384:165–184
pubmed: 26611415
Baker M, Busse H, Vogt M (2000) An automatic registration and segmentation algorithm for multiple electrophoresis images. In: Hanson KM (ed) Medical imaging 2000—Image processing (MI’2000), Proceedings of the SPIE international symposium, vol 3979, 14–17 February 2000, San Diego/CA, pp 426–436
Josso B, Zindy E, Aldemir H (2000) Automatic 2D gel registration using distance minimisation of image morphing. In: Proceedings of the IEEE international conference on information visualization (IV’00), London, England, 19–21 July 2000, pp 357–361
Glasbey CA, Mardia KV (2001) A penalized likelihood approach to image warping. J R Stat Soc B 63:465–514
Rodriguez A, Fernandez-Lozano C, Dorado J, Rabuñal JR (2014) Two-dimensional gel electrophoresis image registration using block-matching techniques and deformation models. Anal Biochem 454:53–59
pubmed: 24613260
Lin D-T (2010) Autonomous sub-image matching for two-dimensional electrophoresis gels using MaxRST algorithm. Image Vis Comput 28:1267–1279
Worz S, Winz M-L, Rohr K (2009) Geometric alignment of 2D gel electrophoresis. Images Methods Inf Med 48:320–323
pubmed: 19499142