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Pathway level analysis of gene expression using singular value decomposition |
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| Authors: | John?Tomfohr,Jun?Lu,Thomas?B?Kepler author-information" > author-information__contact u-icon-before" > mailto:kepler@duke.edu" title=" kepler@duke.edu" itemprop=" email" data-track=" click" data-track-action=" Email author" data-track-label=" " >Email author |
| Affiliation: | (1) Department of Biostatistics and Bioinformatics and Center for Bioinformatics and Computational Biology, Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA |
| Abstract: | BackgroundA promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes). Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications. |
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