Additionally, reanalysis of cell line RNA-Seq datasets using more conservative low expression cutoffs, newer short-read aligners, and copy number callers (Boeva et al. 2012; Langmead and Salzberg 2012; Kim et al. 2013) showed consistent partial compensation ≤1.2-fold in most cell lines (H. Lee and B. Oliver, unpublished data).
The low expression tags cutoff of 100 counts per million was normalized for the number of genes in the THP-1 genome.
Numbers of DEGs selected from the 2657 low expression genes with different cutoff p-values by each method.
For discrimination between a high or low expression, we chose a cutoff value of 100, which was based on the differences in expression between patients who developed metastasis and patients without metastasis.
TYMS overexpression analysis also showed a tendency toward correlation between overexpression smoking (P = 0.056) and histology (P = 0.071) (Fig. 2b), but was not associated with gender, performance status, or line of treatment.> We found that patients with a low level of TYMS gene expression (cutoff < 2.55) had a significantly longer TTP than those with a high level (Fig. 3).
Nine genes at the FDR cutoff (.049-.05) with low expression and fold-changes, and falling into the three main expression patterns, were selected for verification.
To determinate high and low expression of IL-11, the optimal cutoff value was estimated by X-tile plots v3.6.1 (Yale University, New Haven, CT, USA) 16 to achieve the minimum P-value.
Viale et al. [ 31] showed that immunoreactivity of EGFR may have different prognostic values at different cutoff points, and low expression of basal biomarkers may not necessarily lead to poor survival.
Sensitivity was defined as the probability that a patient having low expression of 14q32.31 miRNA (below the cutoff) to be in the high-risk group and specificity as the probability that a patient with high expression of 14q32.31 miRNA (above the cutoff) to be in the low-risk group.
