Explorative data analysis of two-dimensional electrophoresis gels.
Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.
Schultz
Jakob
J
BioCentrum-DTU, Biochemistry and Nutrition, Søltofts Plads, Technical University of Denmark, Kgs. Lyngby, Denmark.
Gottlieb
David Mark
DM
Petersen
Marianne
M
Nesic
Ljiljana
L
Jacobsen
Susanne
S
Søndergaard
Ib
I
D003952:Diagnostic Imaging; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D005782:Gels; D015999:Multivariate Analysis; D011506:Proteins / Q000032:analysis / Q000302:isolation & purification*; D014908:Triticum / Q000737:chemistry
D005782:Gels; D011506:Proteins