TitleSRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets
Publication TypeJournal Article
Year of Publication2013
AuthorsNavratil V, Pontoizeau C, Billoir E, Blaise BJ
JournalBioinformatics
Volume29
Pagination1348-9
Date PublishedMay
Abstract

MOTIVATION: Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV-Statistical Recoupling of Variables-algorithm as an open-source Matlab and GNU Octave toolbox. SRV allows the identification of similarity between consecutive variables resulting from the high-resolution bucketing. Similar variables are gathered to restore the spectral dependency within the datasets and identify metabolic NMR signals. The correlation and significance of these new NMR variables for a given effect under study can then be measured and represented on a loading plot to allow a visual and efficient identification of candidate biomarkers. Further on, correlations between these candidate biomarkers can be visualized on a two-dimensional pseudospectrum, representing a correlation map, helping to understand the modifications of the underlying metabolic network. AVAILABILITY: SRV toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) and in GNU Octave. It is available free of charge at http://www.prabi.fr/redmine/projects/srv/repository with a tutorial. CONTACT: benjamin.blaise@chu-lyon.fr or vincent.navratil@univ-lyon1.fr.

DOI10.1093/bioinformatics/btt136
PubMed ID23508967
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