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Acquired MS/MS data were searched with Mascot 2.2 using a significant threshold of 0.01.
Using a significant threshold of P < 0.05 for the contrasts, genes possessing Unigene annotation information and being differentially expressed in four comparisons were selected to evaluate the over-representation of biological processes in these comparisons.
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In addition, we repeated the comparison of Wilms patients before and after therapy using all 43 samples and applying unpaired two-tailed t-test, which confirmed the results of the matched samples (no significant miRNA using a significance threshold of 0.05 and FDR adjustment).
We repeated the eQTL analysis using a significant LOD threshold of 4.3, yielding a nominal p value of 5×10−5 [16].
However, only the expression fold change observed for the CAD gene (2.17) was higher than the two-fold change conservatively used as a significant threshold in expression studies [ 29].
Instead of determining a significant threshold using permutation tests, one can simply pick the top- k important SNPs.
In the multivariate analysis, we used a statistically significant threshold of a p value of 0.05.
A significant threshold is used in transplant recipients for predicting CMV disease.
A significant threshold effect existed while using PPV to determine a responder (or nonresponder) to volume expansion.
However, even if MLS may be underestimated by TCS, the ability to detect significant MLS (>0.5 cm in CT scan) with TCS was good in our study, with a sensitivity and specificity around 85% when using a threshold for a significant MLS set at 0.35 cm.
The density of loci showed a slight increasing gradient from the centromere to the telomeres with a positive correlation with the distance to the centromere (Pearson's correlation coefficient r = 0.664), even though this correlation was not statistically significant using a 5% threshold (P-value = 0.07).
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