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For each type of gene expression data, Pearson correlation coefficients for all combinations of genes are calculated, and gene pairs whose correlation coefficient is larger than 0.85 are selected as "co-expressed pairs" for each type of gene expression data.
The scores of the candidate genes are calculated by the neighborhood-weighting decision rule.
The shortest paths between the candidate genes are calculated by Pajek software.
This effect may become even more important depending on how significant genes are calculated from a list of significant SNPs.
Given a pathway, the functional similarity scores between the enriched terms of this pathway and all annotated genes are calculated with different methods.
*the percentages of up- and down regulated genes are calculated based on the total number of transcripts found within each group of genes; bold fond highlights larger values.
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Relative expression of genes was calculated according to Pfaffl method8.
KS values for aligned genes were calculated using the codeml method from the PAML package71.
Relative expression levels of genes were calculated by the ΔCt method47.
The relative expression of the genes was calculated by comparing the cycle times for each target PCR.
The theoretical AMDs of particular genes were calculated by considering the CpG sites near the corresponding TSS one CpG site.
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