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Additional file 3: Wilcoxon Signed Rank test result for expression value and tissue specificity between relic and its orthologous counterpart.
We note that all methods are superior to the BHC result for expression data alone (BHI = 0.323), except for the ChIP only analyses.
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Western blot results for expression of vascular endothelial cadherin and occludin also showed decreased expression of junctional proteins.
Moreover, we found similar results for expression variability and for noise.
The results for expression breadth confirmed its positive relation with both UTRs and introns whereas the correlations for CDS again differed between MPSS (positively correlated) and oligo-array (negatively correlated).
For three other genes, we obtained disparate results for expression when the control and MS samples were pooled for analysis.
The same difficulties are encountered when interpreting the results for expression levels of cyclin D1 and TGF-β3.
The results for expression of genes that were not significantly regulated after syngeneic transplantation according to the array were set to 1.
The results for expression levels/profiles of individual target genes (Oct4, Nanog, and Nestin) were normalized according to the relative concentration of the endogenous standard.
Custom PHP and JavaScript code was written to develop a frontend website to enable BLAST [ 19] searches and to select multiple results for expression display.
Recently, tyramide signal amplification (TSA™) methods have provided FISH protocols yielding satisfactory results for expression and coexpression studies of mRNAs with moderate abundance, for instance peptide coexpression in the central amygdaloid neurons (Reyes et al. 2008).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com