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The pattern of increased methylation in promoters and/or gene bodies for the most weakly expressed genes was also consistent (p < 0.05) when gene expression was examined by tissue type.
Concordance between the three replicates was strongly correlated with microarray signal strength, ranging from virtually 100% for the most strongly expressed genes to almost 0% for the most weakly expressed genes.
In fact, zmpB was the most weakly expressed transcript in the majority of the microarray samples.
Interestingly, QSOX1 was most weakly expressed in transformed normal MCF10A cells which do not form tumors in immunodeficient animals.
Advantage of RNA-seq technique resides in its sensibility, allowing most weakly expressed lncRNAs to be identified.
Clusters 18 and 7 include genes that were either most strongly or most weakly expressed in Co27HT.
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endoA null flies rescued to adulthood by the mutant transgenes UAS-endoSS 40.2B, UAS-endoSSQ 58.1, UAS-endoA66D 68.1 and UAS-endoD151P 15.2 displayed embryonic expression levels that ranged between the level of the most weakly expressing wild type line UAS-endoAwt 77.1.2 and the strong line UAS-endoAwt 53.2 (Figure 4A bottom, lanes 2 6 and 8).
Toward this end, we selected the 100 genes with the most-highly expressed pancRNAs and the 100 genes with the most-weakly expressed pancRNAs, as indicated by RPKM.
To lessen the impact of this artifact, 853 of the most-weakly expressed transcripts (~3.8% of all transcripts), which fell below an arbitrary signal intensity cutoff level of 50, were removed from further analysis.
Among genes most strongly decreased in PP skin (e.g., BTC, WIF1 and THRSP), most were weakly expressed in myeloid-derived cell types, but did show specific expression in epidermis (Additional file 2).
Cluster 11 and 14 were enriched in genes that were most strongly or weakly expressed in Co27LT, and genes related to responses to various stresses and stimuli (e.g. defense, water deprivation and cold responses) (Additional file 7).
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