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Recent genomic studies have illuminated general principles of chromatin organization and deepened our understanding of how promoter sequence and nucleosome architecture may impact gene expression.
Gene deletion may impact gene expression through a multitude of effects, depending on its precise function.
However, other factors that may impact gene expression have not been systematically explored.
10.7554/eLife.00354.009 Figure 4. Loss of DNA methylation at promoters may impact gene expression.
Certain genes are turned on and off at particular time intervals, and any disruption of such highly orchestrated methylation regulation may impact gene expression.
Developers of clinical assays should demand an adjacent section for H & E staining, to confirm diagnosis and assess cellularity which may impact gene expression measurements.
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To help evaluate how SNPs in probes may impact gene-level summaries, we provide, in each population, the number of affected probesets (i.e., containing probes with novel SNPs such that MAF >5%) within each transcript cluster (Supplemental Tables S8, S9).
This could reflect the fact that for some processes such as transcription, Ess1 function may impact genes that are essential and therefore not represented in the screen.
In this analysis, we divided all DMRs associated with genes into three groups (non-CpGi promoter, CpGi promoter, and intragenic CpGi), since as noted by others [ 37, 38], methylation in different gene locations may impact the gene expression regulation differently.
In breast cancer, down-regulation of HOXA5 may impact p53 gene expression, contributing to the oncogenic process [ 32, 33].
In addition to SIFT predictions, VEP identifies variants falling in noncoding and potentially regulatory regions that may impact a gene's expression.
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