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We detected a significant TE-by-'gene set' interaction at the 0.1 level (p = 0.085).
Contextual gene set interaction networks were built with tissue/phenotype/genotype-specificities.
Each resultant contextual gene set interaction network shows both cancer-generic and subtype-specific interactions.
We also identified a contextual gene set interaction network from the gene expression data of TCGA GBM.
The effect of genotypes (RILs) was tested either against global residual or against genotype x set interaction when significant.
Compared to this contextual gene set interaction network, a network of ISA biclusters is also shown in Figure 4-II with the same style of tissue-specificity annotation.
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This shows that our approach of using contextual gene sets can be more proper in identifying condition-specific gene set interactions than using conventional biclusters.
For the first set, interactions-of-interest reflect differences between phases.
For the second set, interactions-of-interest reflect differences between migraine and healthy subjects.
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