Even enforcing a stringent false discovery rate (FDR, 0%) and a conservative fold-change (FC) threshold (2-fold), a large number of differentially expressed genes (DEG) was obtained, with 2,351 up-regulated and 1,610 down-regulated transcripts (see Additional file 1 and Additional file 2), suggesting a highly significant difference in expression profiles between group A and group B in Figure 3B.
A conservative 1.5 fold change in gene expression between two or more cell types was used for further analysis, yielding 232 differentially expressed transcripts.
As the purpose of this analysis was to determine common mechanisms of action across diverse cell lines and xenografts, the choice of a conservative minimum fold change selection of 1.3 was appropriate in that it ensured that hypotheses were supported by clear experimental evidence.
Using more conservative filtering criteria (3 fold change in two or more consecutive time-points) we were unable to detect any transcriptional alterations in either endoneurial or neuronal compartments of diabetic mice.
Li and Wong [ 83, 84] have shown that the lower confidence bound (LBFC) is a conservative estimate of the fold change and therefore more reliable as a ranking statistic for changes in gene expression.
In order to perform an unbiased comparative analysis of the two platforms and knowing that the microarrays have a compressed fold change, we chose two different conservative filters to select differentially expressed transcripts.
For duplications we chose a threshold of 10 consecutive SFP sites with a fold change of greater than 4-fold as a conservative estimate of duplication.
Following a conservative approach, we considered enriched those DE contigs having logFC values (the log2 fold change between tissue-specific vs. whole body relative abundances) of 3 or higher.
Of the 24 reference sequences identified as differentially expressed with the more conservative model, 12 had higher counts in the predator-exposed treatment (mean log2 of fold change = 2.4 ± 1.0), and 12 had higher counts in the non-predator-exposed treatment (mean log2 of fold change = 3.2 ± 1.5).
That is, if the Tea Party movement does have real "enemies" within the conservative fold.
