For example, genomic techniques such as DNA microarray analysis (examining 4968 significant genes) [7] and RT-PCR analysis of formalin-fixed, paraffin-embedded tissues (examining 21 prospectively selected genes) [8] have been used for chemotherapy treatment planning in breast cancer.
Towards this end, we performed whole-genome microarray analysis, examining relative expression levels in adult males and females that: 1) were variable between genotypes, 2) were variable specifically in each sex, and 3) showed either reproductive tissue or somatic expression.
Our microarray analysis examining changes in gene expression as a consequence of G85R expression is novel because the Gal4-UAS binary method affords us the ability to express G85R in specific cells.
Biopsies from tumour and control adjacent to the biopsies for microarray analysis, were examined histologically by H. Sandeck to identify which cell types were included in each specimen and also estimate the relative content of cells of each type (per cent of total cell nuclei).
To verify a portion of the findings from the microarray analysis, we examined the gene expression differences between analyses by quantitative real time PCR.
The quality of the RNA samples used for the microarray analysis was examined using the RNA 6000 Nano LabChip Kit (p/n 5067-1511) on the Agilent 2100 Bioanalyzer (G2938C; Agilent Technologies Inc., Palo Alto, CA, USA).
By microarray analysis, we examined gene expression changes and evaluated the resulting genes of interest (GOIs) for ethanol-related biological relevance, identifying sets of genes to serve as potential biomarkers for alcohol-related effects.
Prior to DNA microarray analysis, we examined the expression of two commonly used house-keeping genes, namely glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and β-actin (supplementary material Table S1), in both hemispheres at 6 and 24 hours.
Bearing in mind this observation, the fact that four of five of the informative tumours showed strong biallelic S100A2 expression and considering that the products of TP73L were scored as significantly tumour over-represented in 24% (nine out of 37) of samples in our microarray analysis, we examined the expression of this gene in this independent NSCLC series.
These results agree with another study which used microarray analysis to examine the effect of HPV31 genome on the transcription of cellular genes.
