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A scale of LOG2 was used for calculating the abundance for each probe set gene for each sample.
Examination of the frequency distribution of reference set gene pairs (Figure 1A) shows that the next most dominant term ("Cell wall organization and biosynthesis", GO 0007047) accounts for <5% of reference pairs, with contributions from remaining terms decaying fairly smoothly.
Another advantage of the method is that it does not start from the original observed data set (gene expression matrix for instance) but from a ranking statistic that already summarizes the relevant characteristic under study.
This is similar to the lack of tandem duplication events in the Arabidopsis and rice SET gene families [ 15].
The data were separately clustered for each probe set (gene) using a modified fuzzy C-means algorithm and two clusters.
These 63 genes made up the 25(OH D BENEFIT gene set (gene set "MS_vitD_genes0.05" in Table 1).
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At the probe set level, we performed two concurrent analyses: a probe set expression-intensity analysis and a probe set gene-level normalized intensity analysis.
Cell fusion can efficiently re-set gene expression in adult lymphocytes [ 17] but it is difficult to remove the host cell nucleus from the fused (usually tetraploid) cell.
MLL is homologous to the Drosophila trithorax gene and both protein products play important roles in epigenetics by perpetuating the chromatin structure through propagating pre-set gene expression signatures, thus conveying the epigenetic information to the progeny.
Several systems-biology studies have recently focused on a select set gene-regulatory circuits, in particular those with feedback control.
Variations in the JmjC-SET and the TPR-SET gene numbers in particular genomes (Fig. 3) are, most likely, due to species-specific deletion/duplication events.
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