A histogram was generated by performing the significance assessment of the Moran's I.
The platform-specific gene lists generated by applying the same significance threshold are finally compared.
The observed proportions of selection genes were normalized by 10,000 random permutations to derive a Z-score for each interval, and then they were ranked against the null distribution generated by permutation for statistical significance (see Materials and Methods).
Card et al. ([2010]) show that the approach we follow would be invalid if the pattern of estimate sign and significance were generated by differences in precision rather than differences in effect size.
These tests give a value from 0 1, indicating the strength of a taxon's association with a particular group, and a significance value generated by a randomization procedure.
Induced and repressed genes were extrapolated from significance lists generated by SAM by identifying the average ratio of median value of the replicates for each gene and selecting genes that had values either above 1.8 or below 0.55.
Second, the p-values generated by the programs reflect the significance of miRNA activity changes.
Figure 4 shows a plot of these fractions generated by varying the p-value significance threshold from 0 to 1.
R square, Adjusted R square, intercept, coefficient, standard error and F significance were generated by standard Summary Report.
The p-values were computed by comparing the observed statistics to the distribution generated by the MCR process and significance level was set as.001 [ 14, 15].
