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On the other hand, we consider that the TTC40 methylation frequency was similar to those previously found for the most defined genes as epigenetically silenced in NPC patients such as RASSF1A, RAR β2, DAP-kinase, and DLEC1 [ 7– 10].
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To distinguish between these possibilities, we used K-means clustering to identify the most clearly defined gene sets according to their average Gcn5 localisation pattern (Fig. 5D).
Because most biologically defined gene sets have some correlation structures in their expression profiles, this assumption mostly boosts some of the gene set scores and increases false positive predictions (Dinu et al., 2009; Goeman and Bühlmann, 2007; Newton et al., 2007).
We defined genes (or gene families) that are neither major-group-unbalanced nor subpopulation-unbalanced to be 'random' genes.
To define the most promising candidate genes from above defined gene list, ToppGENE was used as a gene prioritization and enrichment tool [ 22].
We defined gene conservation from the INERTIA score of the most conserved exon (MI score).
DEGs are most commonly defined as genes with non-zero expression difference between two groups.
From information to knowledge: new technologies for defining gene function.
See Text S1 for defining gene sets.
Response: Most studies define HK genes as those that are ubiquitously expressed in most or all tissues and neglect the heterogeneity of expression level.
Subpopulation-unbalanced genes (or gene families) are defined as genes (or gene families) that are unequally distributed among subpopulations; thus, they can be divided into XI-subpopulation-unbalanced genes (or gene families) and GJ-subpopulation-unbalanced genes (or gene families).
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