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I knocked out each query gene (by zeroing its associated connections) in the network independently, and measured the average shortest distance between nodes as a proxy of the (mutant) network functional connectivity; with larger distances indicating higher pathway isolation.
The authors describe their method as follows "…a larger value indicating relatively higher expression levels of genes in a pathway and therefore a higher pathway activity".
Cells on the inside of the hindgut curve show higher pathway activity than cells at comparable distances from the Upd-expressing large intestine on the outside of the curve (Fig. 3A, white arrows).
The tumors in Cluster 3 had significantly a higher pathway deregulation score for majority of pathways than tumors in Cluster 1 and 2 (shown in red in Figure 2A, positive score difference in Figure 2C).
This group (group1) showed 17%, 4% and 20% deletion in JUN, ERK1 and JAK1 respectively; in contrast, group2 (lower survival rates and higher pathway activity) showed only 11%, 1% and 11% deletion percentiles respectively.
In this manuscript, we never claim that species with fewer SIGLEC genes would have fewer Siglec molecules on their cells, with lower Siglec function, nor that having more genes directly translates in higher pathway activity.
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Stunning views and an awe-inducing sense of scale from the sheer rock walls and dizzyingly high pathway will stay with you long after you've stepped down from the hanging bridge and walked away.
The interactions consistently revealed that when agency thinking was high, pathway thinking was generally irrelevant to our various measures of goal pursuit.
This YS architecture not only rapidly conducted ions and electrons through high pathway porous graphene foam, but also preserved necessary tiny void space on distributed Ge quantum dots, which extremely relieved the decrease in volume energy density.
"Basically all [scenarios] lead to problematic warming, and we have been following a rather high pathway in recent years.
Disrupted pathways are found based on high pathway activity scores across cancers.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com