The analogous values for the 5% false positive cut off were 18 to 65. Microarray coverage of UHRR was 62 ± 3% and 71±3%3% using 1% or 5% false positive cut off, respectively.
When a 1% false positive cut off was used, fluorescence intensity from the yeast control spots varied between 25 and 96 fluorescence units.
Thus, the false discovery rate cut off did not change our results.
The tandem mass spectrometry spectra were searched using ProteinPilot 5.0 (SCIEX) with a Swissprot database containing human, bovine, sheep, pig, rabbit, donkey, horse, deer, sturgeon, cod and stock fish species at 1 % False Discovery Rate (FDR) cut off with an identification focus on biological modifications.
Differentially expressed gene lists were then generated by applying a false discovery rate (FDR -corrected cut oFDR -corrected < 0.05.
To minimize false positive results, a strict cut off for protein identification was applied with an unused ProtScore ≥1.3, which corresponds to a confidence limit of 95%, and at least two peptides with 95% confidence were considered for protein quantification.
Statistical significance of protein expression changes and pRB phosphorylation due to knockdowns via RNA interference were calculated using the ANOVA method: protein expression ~ knockdown effect + biological replicate factor + error A multiple testing correction was performed using Benjamini-Hochberg's method [ 40] with a false discovery rate (FDR) significance cut off of 1%.
In this article, we used smaller cut off to reduce false positive rate.
Here, although no gene sets fell below our false discovery cut-off of 0.05, we did observe borderline up-regulation of gene sets in "mRNA processing reactome" and in the "Regulation of Mitosis" and we were able to validate the up-regulation of several of the leading edge transcripts by qRT-PCR (Figure 5G,H).
These genes were identified by one-way ANOVA for each genes and applying a false-discovery rate q = 0.05 cut off across the tests [ 67].
A separate analysis utilizing a forward/reversed database yielded near identical protein identifications at a 1% false positive cut off (data not shown).
