The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter associated with the percentage of donors whose transcriptomic profile is similar.
Considering the stringency of the Bonferroni correction and the fact that the tests are not independent, the P-value correction is quite conservative.
To identify 'GC3-rich' and 'GC3-poor' genes with high stringency, we set the P value < 1e−5 as a significant threshold.
If the case is lack of power we expect that increasing the stringency of p-value cutoff, will increase the proportion of overlapping genes, and indeed this is the evident when comparing 2 local-eQTL studies (Additional file 1: Figure S10).
Dex-treated samples were compared to mock-treated samples with a stringency of p-value <0.05 determined analogous to Fisher's Exact Test.
We use CNV-seq with two modifications of the default parameters for increased stringency: lower p-value for the CNV calls (10-4 instead of the default 10-3), and higher number of consecutive windows required to call a variation (6 instead of the default 4).
At the highest stringency level (p-value < 1.0e-6), the gametocyte-specific transcript Pf11-1 [Pf3D7_1038400]7_1038400] harbored an impressive 1569 predicted human microRNA binding sites.
For the down-regulated pattern, we lowered the input stringency threshold (p-value < 0.01 and FDR < 0.1) to increase the number of input GO terms for the REVIGO analysis.
As a result, 31,570 ESTs (14%) map to the genome at a high stringency (that is, P-value less than 9 × 10-5).
