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.
Sørensen
Peter
P
University of Aarhus, Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology, PO Box 50 DK-8830 Tjele, Denmark. pso@agrsci.dk
Bonnet
Agnès
A
Buitenhuis
Bart
B
Closset
Rodrigue
R
Déjean
Sébastien
S
Delmas
Céline
C
Duval
Mylène
M
Glass
Liz
L
Hedegaard
Jakob
J
Hornshøj
Henrik
H
Hulsegge
Ina
I
Jaffrézic
Florence
F
Jensen
Kirsty
K
Jiang
Li
L
de Koning
Dirk-Jan
DJ
Lê Cao
Kim-Anh
KA
Nie
Haisheng
H
Petzl
Wolfram
W
Pool
Marco H
MH
Robert-Granié
Christèle
C
San Cristobal
Magali
M
Lund
Mogens Sandø
MS
van Schothorst
Evert M
EM
Schuberth
Hans-Joachim
HJ
Seyfert
Hans-Martin
HM
Tosser-Klopp
Gwenola
G
Waddington
David
D
Watson
Michael
M
Yang
Wei
W
Zerbe
Holm
H
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