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Hence, one way to prioritize is to identify genes with evidence of multiple concerted disruption.
UCB affects a large number of cellular functions and neurological damage appears to be the result of their concerted disruption rather than misregulation of a single pathway.
To determine what are likely key nodes in pathways and functions, we hypothesize that, in addition to being altered frequently (by one mechanism or multiple mechanisms), these genes also exhibit multiple concerted disruption (MCD) in a given sample.
Since not all gene expression changes observed in a tumor are causal to cancer development, we demonstrate an approach based on multiple concerted disruption (MCD) analysis of genes that facilitates the rational deduction of aberrant genes and pathways, which otherwise would be overlooked in single genomic dimension investigations.
Using a strategy to identify genes exhibiting congruent alteration in copy number, DNA methylation, and allelic (or loss of heterozygosity, LOH) status, which we term multiple concerted disruption (MCD) analysis, we find genes representing key nodes in pathways as well as genes which exhibit prognostic significance.
On the other hand, those genes which exhibit multiple concerted disruption (MCD) across all DNA dimensions -- i.e. overexpression of a gene due to increased gene dosage, which led to allelic imbalance, and DNA hypomethylation at the same locus relieving regulation -- may likely have strong biological significance.
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In this study, we have developed a stepwise gene selection strategy to identify multiple concerted disruptions using an integrative genomics approach.
Looking at the other relevant studies for cancer transcriptomics, a large scale expression study presented by Wang et al. identified a set of gene markers for prediction of metastasis for breast cancer [ 14] and followed by Chari et al. demonstrated an approach based on multiple concerted disruptions (MCD) analysis and identified genes and pathways in cancer [ 15].
As attempts at disruption go, this one could be filed under concerted.
Structurally heterogeneous tandem arrays demonstrated that the influence of concerted evolution is mediated by the spatial environment of gene duplicates; it can be prevented by disruption of the repeat structure in the array.
Surprisingly, the fine words prompted concerted action.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com