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ChIP-Seq analysis revealed 6,629 AR binding regions in the cancer genome of PC3 cells with an FDR (false discovery rate) cut off of 0.05.
Using an FDR (false discovery rate) cut off of 0.05, we identified a total of 6,629 AR binding regions in the PC3 cells (Table S3).
Thus, the false discovery rate cut off did not change our results.
Normalized data were analyzed using EDGE [ 26] to generate a list of differentially expressed genes with a false discovery rate cut off of 0.05.
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.
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).
Differentially expressed gene lists were then generated by applying a false discovery rate (FDR -corrected cut oFDR -corrected < 0.05.
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%.
However, here where I am all taken up with my discoveries in traveling and cut off from newspapers and European news, I am blissfully very far away from everything.
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].
As all gene expression changes detected and used for analysis in this study were robust (false discovery rate <0.002, and fold change cut off ±2), extensive validation of gene expression was not performed.
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