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Future microarray analyses utilizing additional controls such as cells grown at a lower concentration of Penicillin G, and cells that are enzymatically stripped of their cell wall might be useful to better pinpoint L-form specific responses.
The relative expression pattern of all eight selected genes resembled respective microarray expression patterns (Table 3) and suggested that microarray analyses utilizing the current array were highly reliable and accurate.
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In analyses utilizing microarray datasets for which replicates were conducted, we utilized expression data values across those replicates to study the effect of variance in gene expression on the final predictions of the model.
These approaches allow identification of more functionally coherent regulatory modules, in comparison with the analyses utilizing microarray data alone (Bernard and Hartemink, 2005; Joung et al., 2006; Kim et al., 2006; Yu and Li, 2005; Zhou et al., 2005).
cDNA samples prepared for microarray analyses were utilized for quantitative real-time PCR (RT-qPCR) validation of global expression analysis.
It should be noted that the present analyses utilized only annulus cells in the microarray expression studies; we currently are adding nucleus specimens so that future work can explore expression patterns in nucleus cells as well as the annulus.
Correlation analyses utilized the Pearson's coefficient.
Our analyses utilized 4 data sources.
Analyses utilized mixed and fixed effects models.
Analyses utilized multivariable linear and logistic regression.
Graphs and statistical analyses utilized Prism (GraphPad).
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