Genes whose EST number of any tissue occupied more than a half of the total values were deemed to specifically express.
Indeed, when only the genes deemed to be expressed on all three platforms were tested, the number of genes differentially expressed (q < 0.1) with gestation by HTA increased from 401 to 636, narrowing the gap with RNA-Seq while still being more than three times lower than the one for DriverMap (Fig. S5).
For the 90 miRNAs deemed to be expressed in HEK293T cells, the levels of expression in the presence and absence of FLAG-Ago2 transfection were very similar, with only a few miRNAs registering changes of around two-fold between the two conditions (Figure 2B).
12,833 genes were deemed to be expressed (>4 reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals.
We examined the correlation between methylation and tissue predominance of gene expression in two ways: by comparing hierarchical clustering patterns of gene methylation and expression, and by querying methylation status of sets of genes deemed to be expressed in a tissue-preferential manner.
From each data set, 558 (day 3), 361 (day 7), and 395 (day 25) genes, respectively, were deemed to be expressed differentially and were uploaded into IPA accordingly.
Candidate genes with average counts per million (CPM) >0.5 were deemed to be expressed and considered potential regulators.
The data were then filtered to remove genes deemed to be expressed at a level below reliable quantification by determining those with a raw signal value below a defined background cut-off value of 100 in all samples.
Dieudonné declared that he'd been put under supervision and deemed unfit to express himself.
Genes with an adjusted P value < 0.01 and an absolute value of log2 (expression fold change) ≥1 were deemed to be differentially expressed.
