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Interestingly we found considerable overlap in gene expression between our Braak stage 6 AD cases and controls.
In validation of this model, we have shown a striking convergence of gene expression between our transformed cells and the data of Santin et al [6], who investigated changes in expression in cervical carcinoma (Kravchenko-Balasha et. al., submitted).
Even if there were differences in urothelial gene expression between our two investigated subgroups, they might be too subtle to be detected.
The difference in basal EHsp100 gene expression between our cultures and those of Bernes, et al. [ 16] may be due to differences in the parasite strains.
In this study, glyoxalase 1 and glutathione peroxidase showed significant differences in expression between our zebrafish lines (Additional File 1: Table S1).
This difference in the degree of progenitor expansion could be due to differences in Yap isoforms or level of expression between our models.
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Among the remaining 30 miRNAs, most differentially expressed miRNAs also showed consistent expression profiles between our data and the reported data.
We found that with a 2-fold-change of expression between treatments our analysis was expected to detect 96.8% of differentially expressed genes.
We used expression level estimates from Cuffdiff2 (Fragments Per Kilobase of transcript per Million mapped reads) to calculate correlations of expression levels between our experimental samples (supplementary fig. S1, Supplementary Material online).
Although we observed overlapping changes in gene expression results between our study and this previous report, we also noticed other differences including reduced activation of interferon related genes.
Interestingly, this latest cluster corresponds to the genes that present the highest expression variation between our two studied conditions (with confirmed qRT-PCRs folds >16) (Table 1).
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