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We considered three aspects of gene expression: tissue variability, expression noise, and median expression between tissues.
We next tested the inverse hypothesis: can the difference in median expression between the X and the autosomes be explained by an evolved difference in the density of testis-biased or testes-specific genes?
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Normalization removes systematic gel intensity differences originating, for example, from variations in staining, scanning time and protein loading by mathematically minimizing the median expression difference between matched spots.
The median expression profiles between clusters were markedly different, representing five distinct transcriptional networks.
Median expression ratios between Treg and Tconv were calculated for individual genes by the 'N-fold regulation'-activity of Analyst.
This analysis compared the differences in the median expression values between groups (no alterations versus any alterations) with 95% confidence.
In four out of eight temporal expression clusters median expression rose between 10 and 20 dpp - a time period that corresponds to the meiotic stages of spermatogenesis.
For each probe, we first averaged across sample replicates, then directly compared the median expression values between the two classes (cancer and normal).
The median expression levels between miRNA and non-miRNA target genes were compared, and the statistical significances were evaluated using Wilcoxon rank sum test.
To account for probes that did not pass the t-test due to high intra group standard deviation, we also selected probes based on median expression difference between the group of interest and the reference group.
The male-biased genes also showed a greater degree of sex-bias: the median expression difference between the sexes was 2.13-fold for male-biased genes and 1.25-fold for female biased genes (Wilcoxon test, P < 0.001).
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