The first approach prioritized the genes based on their differential expression behavior in cells treated with the drug or in disease samples compared to normal samples.
Phospho-flow is highly quantitative [21], [23] and novel network-based screens of complex populations in disease samples can easily be obtained [20].
The heterogeneity in disease samples may limit the ability to interpret our results.
Copy number gain was only observed at gene MDH2, whereas other genes consistently suffered copy number loss in disease samples.
The difference in the frequencies of HLA alleles in disease samples and controls was compared using the Chi-square test or Fisher's exact test as appropriate.
Further studies will determine the proteins differentially expressed in disease samples and investigate their potential as protein biomarkers for early detection of cervical neoplasia.
In chronic periodontitis, 7 biomarkers exclusive to the pathology are suggested, but only 2, a chemokine (C-C motif) ligand 13 (Q99616), 4.97x upregulated in disease samples, and thymidine phosphorylase (P19971), 3.7x downregulated in disease samples, fulfill both requisites proposed for a biomarker, to be exclusive of the disease state and to have an up/down amount ≥3x.
Comparing the pattern of variation identified in disease samples with this catalog of 'normal' variation is a crucial step in the process of determining the disease significance of any variants found.
To enrich for biomarkers likely to be found at elevated levels in the peripheral circulation of lung cancer patients, proteins were prioritized based on predicted subcellular localization (secreted, cell-membrane associated) and differential expression in disease samples.
However on closer reflection utility results varied, with EQ-5D scores being significantly higher in healthy populations, and SF-6D scores being significantly higher in disease samples, thus pointing to differences in scaling and a lack of calibration between utility measures [ 71].
