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When we examined expression of a given gene when hemizygous, compared to the median expression of that gene in all lines (by bootstrapping), we observed a much more consistent dosage response, characterized by a strong decrease in median expression, with a median compensation level of ∼1.1-fold, in the case of both Dfs of chromosomes X and 3L.
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In comparisons of inter-platform correlation with median expression, genes with very low and very high expression generally had poorer correlation.
A general decrease in median expression level with increasing methylation level was observed for all three gestational ages.
The remainder not found consisted of transcripts that we removed from the data set due to low median expression level, with the exception of 3 transcripts that were not identified in our analysis.
Samples from the ExpO expression dataset were clustered based on the expression of neuroendocrine genesets (Hes6, Hes6-Chga, Hes6-Ddc, Ascl1, Ascl1-Hes6-Nts-Ddc). Clusters were defined by a median expression level with a threshold level three-fold greater than the average intensity across all samples.
While genes with HP inheritance patterns show the highest median expression levels, genes with LPMP and LP patterns show relatively low median expression levels.
A, Heatmap of expression correlations between pairs of clusters from this study and human cortical clusters reported by Lake et al. 22 based on median expression of genes with cluster-specific expression in both studies.
The founder mouse showed a lower median expression level compared with his offspring.
However, median expression of genes with 5mC-enrichment in both promoters and gene bodies was substantially lower than that of non-5mC-enriched genes in all tissues.
In the chicken, the median expression values decrease with increased chromosome length, which can only be partly explained by the higher gene density of the micro-chromosomes.
Then we identified as expressed those genes with median expression value higher than the selected threshold.
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