Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: a proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson’s disease using DIGE.
BMC Bioinformatics. 2006-01-01; 7(1): 475
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1. BMC Bioinformatics. 2006 Oct 26;7:475.
Normalization and expression changes in predefined sets of proteins using 2D gel
electrophoresis: a proteomic study of L-DOPA induced dyskinesia in an animal
model of Parkinson’s disease using DIGE.
Kultima K(1), Scholz B, Alm H, Sköld K, Svensson M, Crossman AR, Bezard E, Andrén
PE, Lönnstedt I.
(1)Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala
University, BMC, Box 594, SE-75124 Uppsala, Sweden.
BACKGROUND: Two-Dimensional Difference In Gel Electrophoresis (2D-DIGE) is a
powerful tool for measuring differences in protein expression between samples or
conditions. However, to remove systematic variability within and between gels the
data has to be normalized. In this study we examined the ability of four existing
and four novel normalization methods to remove systematic bias in data produced
with 2D-DIGE. We also propose a modification of an existing method where the
statistical framework determines whether a set of proteins shows an association
with the predefined phenotypes of interest. This method was applied to our data
generated from a monkey model (Macaca fascicularis) of Parkinson’s disease.
RESULTS: Using 2D-DIGE we analysed the protein content of the striatum from 6
control and 21 MPTP-treated monkeys, with or without de novo or long-term L-DOPA
administration. There was an intensity and spatial bias in the data of all the
gels examined in this study. Only two of the eight normalization methods
evaluated (‘2D loess+scale’ and ‘SC-2D+quantile’) successfully removed both the
intensity and spatial bias. In ‘SC-2D+quantile’ we extended the commonly used
loess normalization method against dye bias in two-channel microarray systems to
suit systems with three or more channels.Further, by using the proposed method,
Differential Expression in Predefined Proteins Sets (DEPPS), several sets of
proteins associated with the priming effects of L-DOPA in the striatum in
parkinsonian animals were identified. Three of these sets are proteins involved
in energy metabolism and one set involved proteins which are part of the
CONCLUSION: Comparison of the different methods leads to a series of
methodological recommendations for the normalization and the analysis of data,
depending on the experimental design. Due to the nature of 2D-DIGE data we
recommend that the p-values obtained in significance tests should be used as
rankings only. Individual proteins may be interesting as such, but by studying
sets of proteins the interpretation of the results are probably more accurate and
PMID: 17067368 [Indexed for MEDLINE]