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Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects

Krogh, Morten LU ; Waldemarson, Sofia LU ; Fernandez, Celine LU ; Valestro, Barbro and James, Peter LU (2007) In Proteomics 7(23). p.4235-4244
Abstract (Swedish)
Abstract in Undetermined

Differential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of... (More)
Abstract in Undetermined

Differential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of proteins with a statistically significant (0.001 level) dye effect were 19, 34, and 23%, respectively. The fractions of proteins with a dye effect above 1.4-fold change were 1, 4, and 6%, respectively. The median magnitude of the dye effect was 1.07-fold change for Cy5 versus Cy3 and 1.16-fold change for Cy3 versus Cy2. The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
2-D gels, DIGE, dye effects, linear mixed model
in
Proteomics
volume
7
issue
23
pages
4235 - 4244
publisher
John Wiley & Sons
external identifiers
  • WOS:000251664400003
  • Scopus:37049039722
ISSN
1615-9861
DOI
10.1002/pmic.200700339
project
CREATE Health
language
English
LU publication?
yes
id
5e49d6ff-d6d7-4570-87e1-59c4383aa167 (old id 599959)
date added to LUP
2008-01-10 08:21:04
date last changed
2016-10-13 04:51:08
@misc{5e49d6ff-d6d7-4570-87e1-59c4383aa167,
  abstract     = {<b>Abstract in Undetermined</b><br/><br>
Differential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of proteins with a statistically significant (0.001 level) dye effect were 19, 34, and 23%, respectively. The fractions of proteins with a dye effect above 1.4-fold change were 1, 4, and 6%, respectively. The median magnitude of the dye effect was 1.07-fold change for Cy5 versus Cy3 and 1.16-fold change for Cy3 versus Cy2. The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments.},
  author       = {Krogh, Morten and Waldemarson, Sofia and Fernandez, Celine and Valestro, Barbro and James, Peter},
  issn         = {1615-9861},
  keyword      = {2-D gels,DIGE,dye effects,linear mixed model},
  language     = {eng},
  number       = {23},
  pages        = {4235--4244},
  publisher    = {ARRAY(0xade9720)},
  series       = {Proteomics},
  title        = {Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects},
  url          = {http://dx.doi.org/10.1002/pmic.200700339},
  volume       = {7},
  year         = {2007},
}