Similarly, essential genes are enriched for negative TE selection while underrepresented for positive TE selection.
We find that genes whose expression negatively correlated T-DMRs are enriched for functions carried out in adult tissues, while the positively correlated genes were enriched for negative regulators such as transcriptional repressors.
Interestingly, the putative target genes of the positive T-DMR are enriched for negative regulators such as transcriptional repressors, suggesting a novel mode of indirect DNA methylation inhibition of expression through transcriptional repressors.
Another trend that we observed was that cis effects are enriched for negative correlations (65.4% overall) while positive correlations between DNA methylation and gene expression are more frequently observed with trans associations (68.2%; Fisher's Exact test for count data p<2.2e-16 p<2.2e-16onAdditional filere S1b).
Importantly, transcriptome information may not only help to resolve many ambiguous false positive cases but also help identify false negatives, as the inconsistent dsRNAs that have been ruled out to be due to false positives should be enriched for false negatives.
In particular, we hypothesized that the post-chemotherapy specimens would be enriched for NE marker negative cells because of the increased sensitivity of NE positive cells to chemotherapy.
Second, the high-risk HIV-negative cohorts likely to be recruited for vaccine trials might be enriched for genotypes that confer protection.
The basal-like sub-cluster, characterized by the under-expression of these genes, is enriched for triple-negative (hormone receptor and HER2-negative) cancers and contains all cancer tissues of patients that are deceased (black dots) or have recurred (orange dots).
Since the NKI295 data set was enriched for node-negative tumors less than 5 cm in diameter, tumor size and node status were not significant in the multivariate analysis [ 33, 34].
The Claudin-low subtype has been described as BC entity [ 8, 48], which is enriched for ER-negative invasive ductal carcinomas, while displaying low levels of luminal differentiation markers and activation of pathways involved in epithelial-to-mesenchymal transition, stem cell-like features and the immune response [ 8].
