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Significant difference between sample groups was identified using the method described by Storey & Tibshirani [ 24].
A repartition difference between sample groups was considered significant when the Kruskal-Wallis nonparametric test and Wilcoxon test gave a P value ≤0.05.
For RT-PCR, the relative difference between sample groups was calculated according to the difference in Ct values using 2−Δ Δ Ct) (31).
Differential expression between sample groups was assessed using the moderated t-test with p-value correction for multiple testing at a false discovery rate (FDR) threshold of 5% (q < 0.05).
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Comparisons between sample groups were performed using GeneSpring GX 9.0 software (Silicon Genetics, Redwood City, CA).
Statistically significant differences between sample groups were determined using a Student's t-test or ANOVA where applicable, with a p-value≤0.05 considered to be statistically significant (p≤0.05 = *, p≤0.01 = **, p≤0.001 = ***).
Comparisons of expression levels between sample groups were carried out with lineal regression.
Gene expression differences between sample groups were analyzed using t-test or paired t-test.
Significant differences between sample groups were identified by the 'limma' package [ 16].
The following comparisons between sample groups were made: SCC vs. NS, SCC vs. AK and AK vs. NS.
Differences in the frequency of individual CNIs between sample groups were compared using the χ test.
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