Analysis of the real EADGENE data set: multivariate approaches and post analysis (open access publication).
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.
University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, PO Box 50 DK-8830 Tjele, Denmark. pso@agrsci.dk
Peter
P
Sørensen
Agnès
A
Bonnet
Bart
B
Buitenhuis
Rodrigue
R
Closset
Sébastien
S
Déjean
Céline
C
Delmas
Mylène
M
Duval
Liz
L
Glass
Jakob
J
Hedegaard
Henrik
H
Hornshøj
Ina
I
Hulsegge
Florence
F
Jaffrézic
Kirsty
K
Jensen
Li
L
Jiang
Dirk-Jan
DJ
de Koning
Kim-Anh
KA
Lê Cao
Haisheng
H
Nie
Wolfram
W
Petzl
Marco H
MH
Pool
Christèle
C
Robert-Granié
Magali
M
San Cristobal
Mogens Sandø
MS
Lund
Evert M
EM
van Schothorst
Hans-Joachim
HJ
Schuberth
Hans-Martin
HM
Seyfert
Gwenola
G
Tosser-Klopp
David
D
Waddington
Michael
M
Watson
Wei
W
Yang
Holm
H
Zerbe
D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D002417:Cattle / Q000235:genetics; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D004927:Escherichia coli Infections / Q000235:genetics / Q000662:veterinary; D005060:Europe; D005260:Female; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D054884:Host-Pathogen Interactions / Q000235:genetics; D008414:Mastitis, Bovine / Q000235:genetics; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D013203:Staphylococcal Infections / Q000235:genetics / Q000662:veterinary