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First, we implemented a 1.3 fold cut off on the iTRAQ ratios to segregate proteins into those that were up or down regulated.
Similarly, the down-regulation of a putative CPC gene (Contig16590) was below the 2 fold cut off but was statistically well supported (probability = 0.04).
A gene list was then generated using an FDR (Benjamini Hochberg) [ 18] of 0.05 and a 2 fold cut off for fold change.
We used a fold cut off of 2.5 and Students t-test with P-value ≤ 0.05 ranking with false discovery rate (FDR) multiple testing corrections to identify differentially expressed genes.
Similar(56)
Presence/absence calls were made based on a 2-fold cut off.
The data was from 3 biological replicates, statistically filtered (P = 0.05) and a 2-fold cut off applied.
We used two-fold cut off as a simple heuristic to estimate the number of differentially expressed genes.
As mentioned above, the RP genes were also significantly induced by N or P repletion, but they failed to pass the 2-fold cut off.
Gene expression analysis via microarray revealed that over 67 genes were affected in response to 5-FU (n = 3, p < 0.05 with 4-fold cut off).
In the case of EGR1 and ITGA1, the use of GAPDH as reference gene resulted in the underestimation of target genes expressions, leading to false negative conclusions when a two-fold cut off was applied.
A two fold cut-off at a Pval of 0.05 was employed to find out significant genes.
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