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].
AGP related DEGs were downregulated in FLA17 and upregulated as was seen in FLA1 (top expression in yellow stage).
Since some protein sequences are 5′ truncated or predicted starting from an upstream point, we manually checked the prediction of top expression of transcripts containing signal peptides.
(B) Top: Expression of p-EGFR, p-AKT, α-SMA, cyclin D1, and p-Smad in sectioned rat liver was examined by immunohistochemistry.
The top expression quartile of genes from [41] harbors somewhat wider peaks than the lowest quartile (means: 176 vs. 172 bp, respectively, p = 0.002; Figure 8).
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.
Despite this, the exact binding profiles of CHD1 and CHD2 at transcription start sites of genes in the top expression quintile differed.
Top : expression plot, the grey line represents the average expression levels of the genes in all the conditions in this meta-study, the numbers identify the conditions in the biclusters.
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).
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.
