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In contrast, most (4 of 6) of the reference genes were disqualified as appropriate reference controls based on fold changes that exceeded this range at more than one contiguous time point with GAPDH and TfR displaying marked increases (>4-fold) clearly indicative of biological variability.
In particular, fbn-1 is notable in that it is one of only 12 genes within the intron-up category, and, based on fold changes, is the third most highly misregulated gene in the tiling array data set (Supplementary file 3).
Other previously described methylated genes in prostate cancer, such as CDKN2A, PTGS2, and RUNX3, all showed evidence of methylation based on fold changes and statistical significance.
For the comparison of posterior hypothalamus between narcolepsy and control, the top 100 SAM up or down regulated candidates were selected and sorted based on fold changes: those above 2.5 or below 0.4 fold change were studied further.
Next we plotted ROC curves based on fold changes reported by these methods.
For comparative analysis, data were filtered based on fold changes of two or more (either up- or down-regulated).
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Famulski's gene score is based on fold change and is thus dependent on reference gene expression data, for example from control samples.
Ultimately, 22 miRNAs were selected based on fold change as candidate risk factors for ARDS from the logistic regression model (Table 1).
We first filtered the gene list generated with Gene Spring GX 7.3.1 based on fold change between the DMSO and LY294002 treatments.
We selected 19 genes (20 probes) for validation by QRTPCR, including 14 genes for T and 5 for NT tissue, based on fold change (>2) and cancer relevance.
Skov-3 tumor proliferation was measured based on fold change compared to normal Skov-3 cell proliferation in low serum media as detailed in the methods section.
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