The empirical ratio is smoothed with locally weighted regression (solid lines) and compared with a baseline obtained by random shuffling of genders (dashed lines).
For larger primes, it is hard to not produce low correlation p × p sets by random shuffling of the parent Hadamard, as the gap between lowest and worst cross-correlation values is so large, and 91% of random shuffles have either 0 or ± (p + 1) toggle differences.
To select the k value, 200 random networks were generated by random shuffling of the gene names of the nodes in G. DEGAS was then executed on each network, for a range of values of k, and an empirical p-value was computed as the fraction of these 200 networks in which DEGAS found a smaller DP than the one found in the real network.
We did simulation study by random shuffling of miRNA sequences to test whether our method could distinguish a miRNA from its shuffled version during the detecting process.
The statistical significance of this averaged score is assessed by random shuffling of gene GO annotation associations, maintaining both the annotation and gene distribution.
The P-values of the "% of fraction of group m" were calculated with the 200 surrogate data points made by random shuffling of the ranking of head size for cellular groups (Microsoft Excel).
Basically, a total of 10,000 gene pairs were generated by random shuffling of the singleton genes and the Pearson's Correlation Coefficient (r) was calculated similarly for each pair.
This length, though being much less than the average length of protein-coding sequence in plants, is higher than expected to arise by chance (assessed by random shuffling of the contigs with subsequent ORF prediction) suggesting that most of the contigs correspond to protein-coding genes.
After a base-by-base random shuffling of the analyzed sequences, we observed a significant deviation between the real and the randomized data in the genomic signature distances for the LDV-host pairs (t-test, p < 0.001; Fig. 3).
Some of them might indeed represent non-translated regions, but since the average length of predicted ORF in such contigs is significantly higher than in artificial sequences produced by random shuffling, we suggest that most of them correspond to protein-coding sequences, either lineage specific or highly variable.
