To achieve our objectives, we used a variety of techniques: cDNA arrays to identify a discriminatory gene expression signature, real-time quantitative PCR (RTQ-PCR) to examine gene expression at the transcript level, and tissue microarrays (TMAs) with immunohistochemistry to look at protein expression levels of the candidate markers in a first cohort of breast tumor samples.
The MFH/UPS, leiomyosarcoma, and MPNST were characterized by discriminatory gene expression signals containing 90 – 300 genes with FDR of 11%.
We have identified discriminatory gene expression signatures working both on untreated and systematically treated primary breast cancer patients with the potential to spare them from adjuvant therapy.
In order to remove the features (genes) that show no or minimal discriminatory ability, gene expression data are firstly processed with log2 transformation and then differentially expressed genes are determined by two criteria, fold change of expression level as well as P value of Student's t -test.
Microarray analysis of these primary tumours identified a list of 70 discriminatory genes whose expression patterns, in an internal validation, identified a group of patients who had not developed metastases at 5 years from diagnosis despite no systemic treatment.
Our method derives discriminatory rules from miRNA expression data as the first step, and derives discriminatory rules from mRNA expression data as the second step.
When we extended our analysis to the 235,234 non-annotated transcript clusters (many of which probably represent noncoding genomic regions), the discriminatory power of the expression changes dropped sharply (data not shown).
The first step works on the miRNA data of the HCV negative and positive tissue samples to derive differentially expressed miRNAs and discriminatory rules (i.e., the miRNA expression changes between the two classes of samples).
Returning to the case of the Roma who were excluded by the policy of a bar, we could say that the policy was discriminatory because it was the expression of prejudice against the Roma, whereas a bar's policy of excluding men from the women's restroom would fail to be discriminatory because it would not be an expression of prejudice.
Furthermore, if stromal or stromal-interface gene expression does carry discriminatory information, then microdissection would result in loss of predictive information.
