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Encoded by mRNAs consisting of more than 3,300 total codons, both Brca2 and Vcan fall within the largest 1% of all genes detected in our proteome analysis out of more than 17,000 genes (not shown).
In contrast, comparable repeats are largely absent for single-copy genes (not shown).
No such subpopulation was present in other gene groups as well as in LAIR-distal genes (not shown).
Of note, identical results were obtained with two sources of siRNA targeting different sequences of α4 and α5 integrin genes (not shown).
We computed a summary statistic for each team using the geometric mean of the 50 p-values for the individual genes (not shown).
However, at this concentration, treatment with THZ had no impact on the expression of any of these three genes (not shown).
Protein lists were uploaded in DAVID and compared to a random background data set (shown) or a random set of muscle genes (not shown) with comparable results.
Dot plots of heat shock genes (not shown) did not reveal any repetitive sequence comparable to that observed in this study.
Codon bias is unlikely to explain this difference in Ks because the two species groups have very similar codon usage both for these genes (not shown) and, with the exception of D. willistoni, in general [35].
The only two tandem repeat genes not shown to be trans-spliced may not have been present in the cDNA used, based on negative results with gene specific primers.
Compared to uninfected mice, T. gondii infected animals exhibited at least a 2-log increase in mRNA levels of these genes (not shown) and eyes and brains from both infected CD40−/− and infected B6 mice exhibited upregulation of mRNA of these genes at 2 and 4 weeks post-infection (Figure 2A and not shown).
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