An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.
An improved pixel-based approach for analyzing 2-DE images is presented. The key feature of the method is to create a mask based on all gels in the experiment using image morphology, followed by multivariate analysis on the pixel level. The method reduces the impact of noise and background by identifying regions in the image where protein spots are present, but make no assumption on individual spot boundaries for isolated spots. This makes it possible to detect significant changes in complex regions, and visualize these changes over multiple gels in an easy way. False missing values and spot volumes caused by imposing erroneous spot boundaries are thus circumvented. The approach presented gives improved pixel-based information from the gels, and is also an alternative to existing methods for data-reduction, significance testing and visualization of 2-DE data. Results are compared with software using a common spot boundary approach on an experiment consisting of 35 full size gel images. Gel alignment is required before analysis.
Rye
Morten Beck
MB
Chemometrics and Bioinformatics Group, Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway. mortenry@phys.chem.ntnu.no
Faergestad
Ellen M
EM
Martens
Harald
H
Wold
Jens Petter
JP
Alsberg
Bjørn K
BK
D000818:Animals; D002417:Cattle; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008297:Male; D015999:Multivariate Analysis; D009124:Muscle Proteins / Q000302:isolation & purification; D012984:Software
D009124:Muscle Proteins