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Similar observations of varying levels of association were made for many pathways, as can be seen in Figure 3. Based on our analysis of the common cliques, unique cliques, and pathways associated with the cliques for all four populations, gene signatures for CRC can then be developed from the genes identified in these cliques.
Clipper and DEgraph declare so many pathways as significantly activated because they detect sub-graphs, which are portions of signaling circuits of dubious biological meaning.
For instance, Nookaew et al. have proposed to estimate the intracellular fluxes based on the assumption that cells are likely to use as many pathways as possible to maintain robustness and redundancy [ 15].
This analysis revealed many pathways as relevant to sepsis diagnosis, particularly immune activation: Both SIRS and sepsis non-survivors had lower gene expression levels across multiple immune activation pathways.
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GIENA detects over twice as many pathways at q-values < 0.01 as compared to GSA (13 pathways with q-values < 0.01 vs. 6 for GSA), while missing two pathways detected by GSA, with four of the pathways, such as p53, p53 hypoxia, G1 & S phase and RAS, detected by both using the above q-value cutoff.
TF bHLH is regulatory component involved in many developmental pathways as well as in plants metabolism [ 66].
The presence of many incomplete pathways as well as the duplication of pathways on the genomes of all four P. putida strains is striking.
Erk1/2 and Akt signaling are the best characterized targets of the EGF-induced signaling cascade, but EGF regulates many other pathways as well.
In an automated spaceflight, the use of biosensors specific to molecules integrating many pathways such as RhoGTPases should be presented as a simplified and integrated view of cell mechanics.
None the less, the transcript expression assays identified many critical metabolic pathways as well as a key molecular initiating event known to be affected in nitrotoluene exposures identified in protein and nuclear signaling assays, respectively.
CA IX is involved in tumorigenesis through many pathways, such as pH regulation and cell adhesion control.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com