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As a quality filter, we have also specifically chosen to include literature-curated interactions and pathways, but this may bias the network towards disease-associated genes.
Now we are interested only in two-step long pathways but this method can also be used for longer indirect pathways (also in weighted graphs, see [ 17]).
Products have not been observed or characterized for most of these biosynthetic pathways, but this analysis predicts many that are structurally similar to valuable compounds such as vancomycin.
Using GSEA we were able to identify a significant negative mean fold change of genes in a suite of pathways, but this was most consistent in the steroid biosynthesis pathway (ko00100).
The results reported in this manuscript certainly enrich our understanding of the phylogenetic diversity of mevalonate pathways, but this reviewer was not convinced that the findings are particularly surprising.
Genome-wide association studies (GWAS) have implicated many new biological pathways, but this approach has limitations because most of the variants that have been associated with clinical phenotypes, such as adverse drug reactions, are not necessarily causal.
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VDAC's N-terminus has been reported to be a critical feature for activating such pathways, but the structural basis of this role is not understood.
Sex determination is one of the most rapidly evolving developmental pathways, but the factors responsible for this fast evolution are not well resolved.
It is tempting to speculate that these two ncRNA (amongst others) can be direct targets of the SOS response pathway but this remains to be shown.
It is possible that T cell activation inhibits to some extent components of the β-catenin destruction pathway, but this has not yet been established.
The previous experiments support the existence of a Tbx1-|Gata4→Mef2c pathway, but this is not sufficient to explain all our data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com