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Application of partial least squares discriminant analysis to two‐dimensional difference gel studies in expression proteomics
Author(s) -
Karp Natasha A.,
Griffin Julian L.,
Lilley Kathryn S.
Publication year - 2005
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200400881
Subject(s) - linear discriminant analysis , proteomics , partial least squares regression , expression (computer science) , computational biology , chromatography , biology , chemistry , mathematics , computer science , statistics , genetics , programming language , gene
Two‐dimensional difference gel electrophoresis (DIGE) is a tool for measuring changes in protein expression between samples involving pre‐electrophoretic labeling with cyanine dyes. In multi‐gel experiments, univariate statistical tests have been used to identify differential expression between sample types by looking for significant changes in spot volume. Multivariate statistical tests, which look for correlated changes between sample types, provide an alternate approach for identifying spots with differential expression. Partial least squares‐discriminant analysis (PLS‐DA), a multivariate statistical approach, was combined with an iterative threshold process to identify which protein spots had the greatest contribution to the model, and compared to univariate tests for three datasets. This included one dataset where no biological difference was expected. The novel multivariate approach, detailed here, represents a method to complement the univariate approach in identification of differentially expressed protein spots. This new approach has the advantages of reduced risk of false‐positives and the identification of spots that are significantly altered in terms of correlated expression rather than absolute expression values.