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Methods for detecting positive natural selection, like the ones we employed here, are powerful tools to generate and experimentally verify interesting hypothesis on the evolution of new gene functions and phenotypes.
To evaluate the contribution of 34 CpG units to the separation of CIN II/III subjects from CIN I/normal ones, we employed the Random Forest algorithm (see " Methods") in addition to the standard nonparametric statistical method; Figure 5 shows the mean decrease in accuracy (MDA) values of the 34 CpG units, with higher MDA indicating increasing importance of a CpG unit as predictor [ 36].
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It is difficult to compare the expression conditions, as subunit ratios are not specified and plasmid construction is different (in the ones we employ, the original untranslated regions were removed and replaced by those of β-globin).
A common peptide, and one we employed here, is the RGD motif.
For clarity, a priori there is no sensible reason to adopt this strategy versus the one we employed.
This system offers flexibility to tailor the probe groups, such as the one we employed here for miR-15/107 family profiling.
For the latter one, we employed empirical initial state sampling to ensure monostability in the given parameter range (see Additional file 1, section 1).
This software uses a strategy similar to the one we employed; it splits known cDNA or peptide sequences into short fragments and scans the genome.
A genetic screen for naturally occurring modifiers in a sensitized background, such as the one we employed here, should apply equally well in the study of Mendelian or complex disease.
Plasma cyclophilin levels have been assessed earlier in patients with coronary artery disease to study the severity of CAD using an immunoassay similar to the one we employed in our present study [ 14].
While these assays are not identical, those recognizing predominantly the full-length intact molecule such as the one we employed are used extensively by researchers in the clinical field [ 16, 27, 37, 38].
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