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Stable nucleosomes with statistically significant enrichment over the background were identified, using NPS [ 17], for each of the 20 histone methylations and H2A.Z.
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These data provide detailed information on genomic regions enriched in specific histone modifications relative to the genomic background, which were identified using the USeq analysis package (http://useq.sourceforge.net, last accessed October 20, 2014).
Differentially expressed genes for each background correction method were identified using RankProducts (RP) to rank the probesets by fold change [52].
Using the total number of genes presented in the array as a background for comparison, enriched GO terms were identified using a cut-off FDR of <5%.
Using the background corrected probe intensities, TF binding regions were identified using the peak detection procedure described in MAT.
26 bodies were identified using DNA tests.
Recombinants were identified using two methods.
Lipids were identified using internal spectral library.
All elephants were identified using distinctive markings.
Pathways were identified using global test [38].
Repeats were identified using REPuter [57].
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