Typical of ATRX targets, but unusual for CGIs, ATRX-bound CGIs were simultaneously enriched for H3K9me3, H4K20me3, and histone H3.3.
The exception to this general trend is Math1, a gene that appears to be functionally primed in XEN cells being simultaneously enriched for 'active' histone marks (H3K4me2, H3K9ac and H4ac) as well as 'repressive' PRC2-mediated H3K27me3.
Splicing regulators SRp20, SRp30c and SRp75 are simultaneously enriched in 2 clusters (with recurrence ≥3), which are also associated with post-transcriptional regulation.
Moreover, a number of genes were simultaneously enriched in striated muscles, adipose tissue and/or liver, mainly represented by genes implicated in metabolic processes and enzymatic activities.
The use of interaction data to select among hits, consequently, substantially reduces the total number of hits while simultaneously enriching for hits that are more likely to be reproduced in replicate screens.
We show that this method simultaneously enriches for MDA5 stimulatory activity and for a discrete species of antisense RNA mapping to the EMCV L region.
For extracting the specific TFBSs that are enriched in U-CGIs, we took TFBSs that are simultaneously significantly enriched in more than three U-CGI fragments (i.e., half of the counted fragments) as over-represented TFBSs in U-CGIs.
For example, ATAC peaks that became accessible when Prmt5 was knocked down were enriched for H4R3me2.
By definition, these decreased heterozygosity candidate intervals will be enriched for haplotypes carrying the causative haplotype, and other non-causative haplotypes will be simultaneously depleted from the same phenotype pool.
Our goal was to include interactions between altered genes, and to simultaneously identify biologically informative "linker" genes which were not in the original altered list, but which were statistically enriched for connections to member of the GBM gene list.
