Software-induced variance in two-dimensional gel electrophoresis image analysis

2005 ◽  
Vol 26 (23) ◽  
pp. 4508-4520 ◽  
Author(s):  
Åsa M. Wheelock ◽  
Alan R. Buckpitt
Keyword(s):  
Image Analysis ◽  
Gel Electrophoresis ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis

Advances in two-dimensional gel matching technology

2004 ◽  
Vol 32 (3) ◽  
pp. 511-516 ◽  
Author(s):  
S. Church
Keyword(s):  
Nonlinear Dynamics ◽  
Image Analysis ◽  
Gel Electrophoresis ◽  
Two Dimensional ◽  
Analysis Software ◽  
Two Dimensional Gel Electrophoresis ◽  
Software Products ◽  
Large Numbers ◽  
Noise Contamination ◽  
The Impact

For many years, two-dimensional gel electrophoresis has been the method of choice for the investigation of complex mixtures of proteins. Although there are a number of emerging technologies that can be applied to proteomics, none can yet yield routinely the breadth of information available from two-dimensional gels. To be able to obtain instant information regarding molecular mass and pI, as well as to highlight quickly the expression changes or unique proteins across a gel series requires sophisticated and powerful image analysis software. The range of software products offered by Nonlinear Dynamics covers all levels of user application and throughput, from the user-guided Phoretix two-dimensional approach, when working with a small number of gels, to the automatic processing of large numbers of gels with minimal user intervention with Progenesis. Integration of the analysis software with powerful database components allows advanced gel comparisons and data mining to be performed with statistical verification of the results. Spot pick lists can be quickly created and automatically linked to a number of commercially available spot picking robots further increasing the support for proteomics research. The importance of image analysis for accurate, reliable and meaningful results will be discussed. Recent advances in development, with particular attention placed on the impact of noise contamination within gels, are illustrated and how the Progenesis product from Nonlinear Dynamics can be utilized to get the most from two-dimensional gel electrophoresis is shown.

scholarly journals Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler

Medicine ◽  
2020 ◽  
Vol 99 (49) ◽  
pp. e23373
Author(s):  
Jose Arturo Molina-Mora ◽  
Diana Chinchilla-Montero ◽  
Carolina Castro-Peña ◽  
Fernando García
Keyword(s):  
Image Analysis ◽  
Gel Electrophoresis ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis

Protein variability among Portuguese and other populations of Globodera rostochiensis revealed by two-dimensional gel electrophoresis with computed image analysis

Nematology ◽  
2000 ◽  
Vol 2 (4) ◽  
pp. 461-471 ◽  
Author(s):  
Maria Susana Newton De Almeida Santos ◽  
Didier Mugniéry ◽  
Maria José Moreno Da Cunha ◽  
Isabel Maria De Oliveira Abrantes ◽  
Michel Bossis
Keyword(s):  
Image Analysis ◽  
Gel Electrophoresis ◽  
Gaussian Model ◽  
Globodera Rostochiensis ◽  
Computer Assisted ◽  
Two Dimensional ◽  
Protein Patterns ◽  
Two Dimensional Gel Electrophoresis ◽  
Bootstrap Analysis ◽  
Biological Studies

AbstractSilver-stained two dimensional gel electrophoresis (2-DGE) was used to characterize 46 populations of G. rostochiensis and, as an outgroup, one population of G. pallida. Protein patterns of white females were compared with the aid of computer assisted image analysis using Kepler software. A synthetic master pattern of G. rostochiensis, built with spots present in all populations and detected in at least two of three gels of each population, revealed the presence of 379 protein spots. The populations were compared taking into account the main spots present in each isolate (spots present in two of three gels, amplitude greater than 7, volume greater than 500 and with values fitting the Gaussian model). Comparison allowed the identification of 200 polymorphic spots. Similarity indices (F) and genetic distances (D = 1 ­ F) between populations were calculated on the basis of homologous polymorphic spots, and a dendrogram was constructed according to the UPGMA method. Bootstrap analysis was used to assess the significance of the results from the phenetic study. The presence or absence of specific spots in some G. rostochiensis populations is discussed. Further biochemical and biological studies are necessary to determine if specific proteins are linked to virulence. Variabilité protéique de populations portugaises et d'origines diverses de Globodera rostochiensis détectée par électrophorèse bidimensionnelle et analysée par informatique - L'électrophorèse bidimensionnelle (E2D) est utilisée pour caractériser 46 populations européennes de G. rostochiensis et une population de G. pallida, prise comme groupe extérieur. Les protéinogrammes obtenus à partir de femelles blanches sont comparés par analyse informatisée d'images à l'aide du logiciel Kepler. Une image de référence est constituée au vu des taches protéiques détectées dans l'ensemble des populations étudiées par transfert vers cette image synthétique de chaque protéine détectée au moins deux fois sur trois dans une population. Celle-ci permet de répertorier et de localiser 379 protéines. Les populations ont été comparées avec les taches pröteiques les plus importantes (taches présentes dans au moins deux gels sur trois, amplitude plus grande que 7, volume plus grand que 500 et valeurs dans le model Gaussien). La comparaison des populations a permis de détecter 200 protéines. Les indices de similarité (F) et les distances génétiques (D = 1 ­ F) ont été étudiés à partir des taches polymorphes homologues présentes dans chaque population. Le dendrogramme a été construit selon la méthode UPGMA. Une analyse des valeurs de bootstraps a été utilisée pour estimer la signification des résultats phénétiques. La présence ou l'absence de protéines spécifiques de certaines populations de G. rostochiensis est discutée. D'autres études biochimiques et biologiques sont en cours pour déterminer si les protéines spécifiques sont ou non liées à la virulence.

Sign in / Sign up

Export Citation Format

Share Document