Finally, it is also possible that some of the loci reported had a basal copy number that is too high to be correctly measured by MLPA, that is known to reliably distinguish copy numbers between zero and five copies [43], [45], but its sensitivity greatly decreases when higher copy numbers are measured.
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The comparison of miRNA copies between our two deep sequencing libraries was performed according to the Z-test algorithm as described previously [56].
We built an index of the similarity of each copy of these elements compared with the most identical pair of copies between the two genomes, normalized by the size of the copies.
For each TE family, this most identical pair of copies between the two genomes is defined as the pair of copies with the lowest P-values from all the detected copies using the 80-80-80 rulet(Wicker et al. 2007).
These activity tracks are used to rank between 0 and 1 all the copies of each identified TE according to their divergence from the corresponding most identical pair of copies between the two genomes, with 1 corresponding to a low degree of divergence and a recent activity of this TE and 0 corresponding to old and divergent copies.
The raw CNV values were converted into five categories: amplification (copy number of eight or more), partial amplification (copy number between three and seven), normal (copy number of two), partial deletion (copy number of one), and full deletion (copy number of zero).
Genes whose differences in expression varied in the same direction as differences in copy number between two groups (e.g. relative over-expression of genes in a region of increased copy number) were viewed as genes of interest.
In order to identify chromosomal regions with significantly different DNA copy number between two groups of samples, a two-class unpaired t-test was performed using SAM [14].
Differences in expression of a gene of interest or in genomic DNA copy number between two samples were calculated by the comparative Ct or 2ΔΔCt method [ 22, 23].
