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The monocystronic gene ilvC, which is depressed exclusively by valine has a high value of expression score.
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High values of expression were obtained for nrdA (5.2, 11.8) and nrdB (4.4, 13.9) encoding ribonucleotide diphosphate reductase in dnaA and dnaC strains respectively.
We use two measures of expression: breadth of expression (the number of tissues in which a gene was expressed) and maximum expression level among tissues (the highest value of expression of a gene among tissues).
A high value of OPN expression is unfavourable both to survival (risk ratio 1.88 : 1) (P=0.037) (Table 3) and relapse (risk ratio 2.08 : 1) (P=0.013) (data not shown).
Osteopontin expression level was significantly correlated with overall and disease-free survival, both in univariate and in multivariate analyses; so, a high value of OPN expression is seen to be unfavourable both to survival (risk ratio 1.88 : 1) and relapse (risk ratio 2.08 : 1).
The highest values of expression for class I were seen for HDAC8 (2.0 to 6.0).
Furthermore, the recent study has shown higher values of expression in colon cancer (93%) than in rectal cancer (87%), associating this decrease of Cox-2 expression to decreased disease-specific survival and decreased disease-free survival in rectal cancer but not in colon cancer, suggesting the Cox-2 expression as a predictive clinical biomarker of rectal but not colon cancer [ 37].
Similarly, define RD = (Emin2-Emin)/(Emax-Emin), where Emin2 represents the second lowest expression among the family members in tissue T. The ratio RD captures decrease in expression, i.e., high value of RL represents an expression decrease.
For each family of TF (F1, F2, ‥, Fk) and each tissue T, we computed the ratio RI = (Emax-Emax2)/(Emax-Emin), where Emax and Emin represent the maximum and the minimum expression levels and Emax2 represents the second highest expression among the family members in tissue T. The ratio RI captures the increase in expression, i.e., high value of RG represents an expression increase.
We thus set our third criterion for SCN specificity of a gene as a high value of the SCN/Hypothalamus gene expression values.
When going from (i) to (ii) OCT4 exposes NANOG and the high value of LIF (KLF4 over-expression [ 50, 51]) induces NANOG, raising its expression to a sufficiently high level.
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