Technical challenges that particularly affect microarray studies include, e.g. technical errors in the lab, problems with image analysis and normalization.
Several important issues to consider when integrating microarray studies include use of different gene expression measurement scales, varying analytical power and reliability of the results for individual studies.
Genes down-regulated in methanol, as noted in previous microarray studies, include those for glycolytic enzymes and also genes for various anabolic and macromolecule biosynthetic processes (transcription, translation, DNA replication), kinase and phosphotransferase activities (Additional file 1: Figures S19-S22).
The importance of quality control (QC) measures in microarray studies, including pre-chip (RNA quality of samples) and post-chip outcomes of the data, has been described previously [ 19].
We therefore conducted a systematic review of seven microarray studies including our previously unpublished study and confirmed that the general overlap between the studies was indeed poor: only 229 of all 3574 (6%) genes reported to be differentially expressed in MS had been identified in at least two studies, and 94% were therefore unique to a single study.
For a detailed description of our microarray studies, including (limitations and strengths of) study design, sampling, staining, laser dissection microscopy, RNA isolation and stringent quality control, single amplification, labelling and hybridization procedures, see our previous publications of Booij et al. (2009) [ 27] and Janssen et al. (2012) [ 28].
Probes differentially expressed in the microarray study included genes coding for cell wall structure and defense, phytoalexins and 16 of 17 classes of PR proteins (Figure 4, Table 1, Table S2).
A further study microarray study included extra genes from the Canadian PCR-ribotype 027 strain, QCD-32g58 [ 30] [Genbank: AAML00000000]) where the conserved genetic core was defined and divergent regions were conserved amongst strains of the same host origin.
In a recent tissue microarray study including benign nevi, primary and metastatic melanomas, VEGFA, VEGFR-1, and -2 were found to be upregulated in the malignant tumours whereas VEGFR-2 positivity was higher in metastases than in the primary tumours (Mehnert et al, 2010).
The microarrays study included a total of 35 patients with LARC with additional 8 patients in the validation group.
