Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.
BACKGROUND
The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.


RESULTS
Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached.


CONCLUSIONS
It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.
Hedegaard
Jakob
J
Arce
Cristina
C
Bicciato
Silvio
S
Bonnet
Agnès
A
Buitenhuis
Bart
B
Collado-Romero
Melania
M
Conley
Lene N
LN
SanCristobal
Magali
M
Ferrari
Francesco
F
Garrido
Juan J
JJ
Groenen
Martien Am
MA
Hornshøj
Henrik
H
Hulsegge
Ina
I
Jiang
Li
L
Jiménez-Marín
Ángeles
Á
Kommadath
Arun
A
Lagarrigue
Sandrine
S
Leunissen
Jack Am
JA
Liaubet
Laurence
L
Neerincx
Pieter Bt
PB
Nie
Haisheng
H
Poel
Jan van der
JV
Prickett
Dennis
D
Ramirez-Boo
María
M
Rebel
Johanna Mj
JM
Robert-Granié
Christèle
C
Skarman
Axel
A
Smits
Mari A
MA
Sørensen
Peter
P
Tosser-Klopp
Gwenola
G
Watson
Michael
M