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However, the maximum fold enrichment in pathogen targets (black line) occurs when the top 5% of genes are classified as bottlenecks.
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Enriched 6mers exhibited similar enrichment profiles across concentrations, peaking in fold enrichment at concentrations typically between 16 64 nM.
Fold enrichment of a particular gene in a specific human cell type was calculated as follows: the intensity of the gene in one cell type was divided by the maximum of the intensities in the two remaining cell types.
Fold enrichment was determined by the ΔΔCT method.
ERs were ranked by their mean enrichment values (mean fold enrichment of probes for microarray-identified ERs, and fold enrichment over input for sequencing-identified ERs).
The fold enrichment value measures the magnitude of enrichment and is considered significant if 1.5 or above [54].
We also found >2 fold signal in genes previously identified as methylated in prostate cancer such as CDKN2A (average of 15.8 fold enrichment), RUNX3 (2.8 fold), and PTGS2 (2.9 fold).
Such genomic regions were further filtered to include sequences with minimum 1.3 fold enrichment, and minimum −1.3 fold depletion.
Fold enrichment was calculated after normalization with input (no antibody added) of transfected cells.
Fold enrichment is expressed in relation to the value determined for the untreated sample value.
Linear interpolation was used to estimate the fold enrichment at each base position within the window.
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