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Breitling et al. proposed a simple method named GiGA which receives a list of genes ordered by their differential expression significance and extracts subnetworks corresponding to the most differentially expressed genes [31].
To quantity differential gene expression, significance analysis of microarray (SAM) [14] was performed.
Nine genes were significantly differentially expressed (DE) based on B-value (the log posterior odds ratio of differential expression vs non-differential expression; significance was set at B>0) between UL and PL in the parents (Table 1).
bDifferential expression significance P <0.05 for UV factor in ANOVA.
A total of 23,195 microarray probes passed the differential expression significance threshold (see Methods).
But there are limited reports about the expression, significance, function of Nrf2 in HCC.
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After combining methylation and expression significances, genes having FDR<0.01 and having methylation change >15% and >40% are compared.
Pooled dataset results showing Differential Methylation (DMR), Differential Expression (DE), Combination of Differential Methylation and Differential Expression Significances (FDRs Combined) and Methylation Change in %.
Batch230 Results showing Differential Methylation (DMR), Differential Expression (DE), Combination of Differential Methylation and Differential Expression Significances (FDRs Combined) and Methylation Change in %.
We have investigated thyroid cancer-associated genes with respect to their methylation and expression significances in our datasets (Tables 6, 7, 8).
When methylation and expression significances were combined (Model 4, B dataset), p53 signalling pathway was observed at 16th rank with Bonferroni Score 1.51E-12.
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