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The reads per gene values of all genes were calculated from the SAM output files.
The mRNA levels of those genes were calculated using a relative ratio to GAPDH.
The relative expressions of target genes were calculated using the 2ΔC t) method.
The relative expression levels of target genes were calculated using the 2−ΔΔCq method.
Additionally, correlations between known interacting genes were calculated.
Relative expression levels of genes were calculated by using the Pfaffl method [64].
The relative expression ratios of the target genes were calculated as previously described [49].
Copies of the genes were calculated by comparative Ct method in an absolute quantitation assay following standard protocol [19].
If no such overlap was found, the distance to the closest upstream and downstream genes were calculated.
Distances between genes were calculated with a weighted Euclidean metric.
Expression values for annotated genes were calculated as RPKM [ 137].
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