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MG-thymoma exon array permutated data set To perform permutations, the median fold changes of the thymus samples were mixed twice.
The median fold changes in microRNA levels comparing third trimester pregnant women to non pregnant women are detailed in Table 1.
Regardless, at almost all positions the median fold changes are higher for sequences that have a G or C at the respective positions.
The three hundred most up-regulated and down-regulated genes have median fold-change cutoffs of at least 3-fold, though typically the median fold changes are much higher, with a mean of 6-fold for the up-regulated genes and 33-fold for down-regulated set.
Plotting average fold changes rather than median fold changes resulted in very similar relative performances.
The median fold changes in activity were also strikingly high, 2.9-fold and 3.2-fold, respectively.
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Additionally, the median fold change is depicted as a bar to allow for easy comparison between the strains.
Shown is the median fold change for each nucleotide at each position near the a) cap site b) start site or c) stop site.
For that reason we set the minimal median fold change limit at 1.5 instead of 2 (with a p-value ≤0.01).
Assessing a bias in the median fold change of 4 groups (corresponding to the four nucleotides A,C,G,U) was performed using the Kruskal-Wallis test.
Sequences that start with a TOP motif have a higher median fold change (median: 1.2) than those without (median: 1.03) (p = 0.00002, Wilcoxon-Mann-Whitney two-sample rank sum test).
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