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BioMed Central, Genetics Selection Evolution, 6(39), 2007

DOI: 10.1186/1297-9686-39-6-651

BioMed Central, Genetics Selection Evolution, 6(39), p. 651-668

DOI: 10.1051/gse:2007030

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Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)

Journal article published in 2007 by Peter Sørensen, Agnès Bonnet, Bart Buitenhuis, Rodrigue Closset, Sébastien Déjean, Céline Delmas, Mylène Duval, Liz Glass, Jakob Hedegaard, Henrik Hornshoj, Kim-Anh Lê Cao, Ina Hulsegge, Florence Jaffrézic, Kirsty Jensen, Li Jiang and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent ( E. coli or S. aureus ). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following E. coli infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with E. coli but not correlated more than expected by chance when the infective pathogen was S. aureus . The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed.