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We examined those genes meeting a Bonferroni multiple testing correction from this discovery report and did not find overlap with our gene expression findings.
In order to obtain an ex vivo confirmation of the Affymetrix gene expression findings, we selected 18 (upregulated) out of the 36 genes initially differentially expressed, to subject them to a custom-designed real-time PCR Applied Biosystems 7900HT Micro Fluidic Card system.
Dr. Jonathan Kerr, a microbiologist and chronic fatigue expert at St. George's University of London, said the C.D.C.'s gene expression findings last year were "rather meaningless" because they were not confirmed through more advanced laboratory techniques.
The immunostaining results are in line with our corresponding gene expression findings as verified by the microarrays.
To corroborate our gene expression findings, we also examined ERα protein expression in the TA muscle, and protein expression mimicked gene expression.
Although this study contains a replication of the genetic findings, it remains limited due to the lack of replication of the expression findings, thus warranting further studies.
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Using the RNA-seq data, nine of these genes were categorized into quartiles of expression, finding that all of the genes were expressed at high levels (Additional file 1: Figure S7).
Finally, we explored the ability of FgaA and FgaB to shut down Sima-dependent gene expression, finding that, although the two isoforms are active, the regulatory capacity of FgaB is clearly stronger than that of FgaA.
Another example of an unexpected expression finding was the lack of activation of the structural components of cable pilus operon of B. cenocepacia J2315.
Including half the probes in a split set, about 7.8% of probes will produce a different gene expression finding than the majority of probes designed for each gene.
We believe that these Mad3p over-expression findings are relevant to human disease.
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