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The transcription value of PPAR δ was determined by plotting on a standard curve constructed using HCT116 colon cancer cells.
The fold change for a particular target was determined by comparing the relative transcription value of the treatment with that of the control.
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Table 1 shows the mean relative transcription values of the five genes, comparing in vivo and in vitro expression.
Transcription
Relative transcription values were calculated as described on the legend to the table 1.
Relative transcription values of 97 genes were obtained (Additonal file 3).
To achieve this, the log2 transformed expression values originally downloaded were reverse log transformed to comparative transcription values.
WT1 transcription values were normalized against the expression of β -actin, to adjust for variations in RNA and cDNA synthesis.
The permutation test is carried out after standardizing the transcription values of genes annotated to the specific pathways.
Transcription values were converted to ratios by dividing the value reported in each experiment by the probe set mean value in all experiments in a dataset.
The resulting transcription values for each gene were also normalized for primer pair amplification efficiency using the Q-PCR values obtained with Input DNA (unprecipitated genomic DNA).
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