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Bioinformatics Advance Access originally published online on November 3, 2008
Bioinformatics 2009 25(1):42-47; doi:10.1093/bioinformatics/btn574
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Shortest path analysis using partial correlations for classifying gene functions from gene expression data

A. Marie Fitch * and M. Beatrix Jones

Institute of Information and Mathematical Sciences, Massey University, Auckland, New Zealand

*To whom correspondence should be addressed.


  Abstract

Motivation: Gaussian graphical models (GGMs) are a popular tool for representing gene association structures. We propose using estimated partial correlations from these models to attach lengths to the edges of the GGM, where the length of an edge is inversely related to the partial correlation between the gene pair. Graphical lasso is used to fit the GGMs and obtain partial correlations. The shortest paths between pairs of genes are found. Where terminal genes have the same biological function intermediate genes on the path are classified as having the same function. We validate the method using genes of known function using the Rosetta Compendium of yeast (Saccharomyces Cerevisiae) gene expression profiles. We also compare our results with those obtained using a graph constructed using correlations.

Results: Using a partial correlation graph, we are able to classify approximately twice as many genes to the same level of accuracy as when using a correlation graph. More importantly when both methods are tuned to classify a similar number of genes, the partial correlation approach can increase the accuracy of the classifications.

Contact: m.fitch{at}massey.ac.nz

Associate Editor: David Rocke

Received on August 10, 2008; revised on October 14, 2008; accepted on November 2, 2008

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