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Three replications were performed to obtain average values and standard deviations of expression level for each gene.
Wang et al. [ 17] standardized gene expression levels based on the means and standard deviations of expression measurements from the arrays of healthy prostate samples.
The estimated (across arrays) standard deviations of expression levels for each gene can be summarized by reporting their average across genes for each of the six test-sites.
In both cases we observe similar distributions of standard deviations of expression levels across tissues between imprinted and non-imprinted genes (background) on the array [see Additional file 2].
In order to dissect the pattern, we computed GC3 and the standard deviations of expression levels for 15,625 O. sativa genes across 106 series of gene expression measurements (see Methods).
Relative changes in mRNA expression were normalized to DNA polymerase β as a housekeeping gene, and the data were Z-score-transformed to show deviations of expression in standard deviation units [ 26, 37].
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For each class, we calculated the sample-specific ratios of un-expressed exons, and the mean and standard deviation of expression levels for the exons with minimum post-transcriptional retention (i.e., at least one read was mapped on the genomic region).
Bars depict the average and standard deviation of expression level normalized to XA21 of two technical replicates.
Bars depict the average and standard deviation of expression level normalized to Kitaake mock treatment of two technical replicates.
Bars depict the average and standard deviation of expression level normalized to XA21 of three technical replicates.
Expression values are in log2 scale; SD = standard deviation of expression values.
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