Therefore, these gene expression changes are "consensus" fold changes across multiple microarray studies following adjustment of confounding variables in individual studies.
An analogous strategy of C. elegans was observed by DNA microarray studies following single compound exposures to PCB52 [ 11] and Cd [ 12].
Human miRNA Microarray V3 kits (G4470C, Agilent Technologies) were employed for this study following manufacturer's protocols.
All significant genes identified by the current microarray study were up-regulated following pathogen exposure for one or both strains.
We show that experimental design and environmental confounders greatly influence the identification of candidate genes in ecological microarray studies, and that following several simple recommendations could facilitate the analysis of microarray data in ecological settings.
The sampling date was two days following the microarray study sampling date.
From the microarray study, transcripts were selected by the following criteria: i, probe sets with a fold change >2, ranked after significance level (p = 0,1E-05 0,1E-05; calculatod by ttest, [ 22]), ii, lower expression in unfavourable compared to favourable tumours.
All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus.
Our studies were limited to a small number of published microarray studies for which the following criteria were true: 1) A reasonably large number of biological replicates were analyzed.
Furthermore, other microarray studies have shown that following an acute exposure to TCDD, the majority of these genomic biomarkers exhibit a similar response as that seen in our study [ 14, 29, 30], thus providing further evidence for their roles as biomarkers.
Therefore it is possible that the microarray results reflect cross-hybridisation of different, but related transcripts, although a previous microarray study has also reported a decrease in PPARγ mRNA following VO feeding in salmon [ 35].
