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Genes from our dataset were ranked by their average fold difference in expression between OSE to CEPI.
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All were upregulated in CIN3 by an average fold change of 2.3 (2.3 – 3.3).
The fold coverage for each 500-bp bin was determined, and the fold coverage in each 500-bp bin was divided by the average fold coverage across the genome.
The relative expression level of RGS4 mRNA in the STG from the cohort used in this study has been previously reported as significantly down-regulated by an average fold change of -1.93 by relative real-time PCR [ 31], which was confirmed in the current study as a significant down-regulation of -1.79 fold by microarray analysis.
The analysis showed that, among the 1011 miRNAs, the miRNA expression levels of 20 (2.0%) in MiaPaCa2-RGs (Supplementary Table S2) and 74 (7.3%) in PSN1-RGs (Supplementary Table S3), respectively, were altered by >1.5 average fold relative to parental, keeping adequate expression quantities and excluding miRNA*s.
Thus, selection by permutation analysis is more stringent than selection by average fold change and t-test.
A dendrogram of the putative σB promoter sequences showed no apparent clustering of these promoter sequences by either average GEI in 10403S or by σB-dependence (average fold change).
Genes were then sorted by average fold change.
Genes were ranked by average fold change over 12 hours and 24 hours of glutamine starvation compared to normal control.
First, the differentially expressed genes between suicide completers vs. non-suicide groups were filtered by average fold change (FC ≥ |1.3|) using the BRB-array tool[ 30] without covariates.
In the spleen, 36 genes were identified that were induced twofold by adjuvant treatment (average fold change; Table 3).
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