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They demonstrated that with most methods, over 90% of differently expressed genes at the top expression levels could be detected with using two replicates and 5% of the reads [ 30].
Additionally, we pursued high top expression levels (more than 100 reads) of these genes in any one of the mentioned conditions (only one quarter of the genes showed this expression level or higher).
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In fact, all RP genes in E. coli do not reach the top expression level.
Additionally, we filtered for greater than 100 reads in the top expression level in the higher condition.
As expected, we found that H3K4me3 enrichment was most pronounced around the 5' region of genes in the top expression level category, showing a concordant decrease with less abundant transcript levels.
Gametocyte-stage specific expressed genes were defined as all genes among the top 30% expression levels at the gametocyte stage and the bottom 50% expression levels in all other stages.
cGenes that showed top ranking expression levels when genomically amplified.
Six genes; NUP153, AOF1, DEK, SOX4, FAM8A1, and MBOAT1 showed top ranking expression levels when amplified.
Expression profiles were categorised into four quartiles, with the highest quartile representing the genes that had the top 25% expression levels prior to DAC treatment.
We note that in the analysis we eliminated the genes within the bottom or top 5% expression levels, which may be largely attributed to background or saturation noise.
Among the 13 genes in the 2p25 amplicon for which expression data were available, six genes showed top ranking expression levels when amplified, ITGB1BP1, CPSF3, ADAM17, YWHAQ, TAF1B and RRM2.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com