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iPath/iPath2 has been extensively used for customized pathway rendering and visualization of experimental data and can conveniently be employed to visualize differential usage of pathways in a global pathway map (for typical applications of iPath2, see, for instance, Navid and Almaas 24 and Erickson et al 25).
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10.7554/eLife.07186.007 Figure 3. FGF and PDGF transcriptional responses exhibit differential usage of intracellular pathways.
Based on this review, we address potential barriers which may impede implementation and suggest interventions which may increase the uptake and usage of care pathways.
Thank you for sending your work entitled "Receptor tyrosine kinases modulate distinct transcriptional programs by differential usage of intracellular pathways" for consideration at eLife.
Altogether this idea reinforces the hypothesis that the cyanobacterial TCA cycle performs a crucial function in producing precursor metabolites for biosynthetic reactions (Zhang and Bryant 2011) and that the usage of alternative pathways for respiration requires the presence of 2-oxoglutarate completing the cycle (Araújo et al. 2010).
In order to locate in which pathway our up-regulated and down-regulated genes are enriched, we relied on the usage of KEGG pathway for this analysis.
We calculated the average number of observed seniors in all observations to represent usage of each pathway segment.
The study investigator performed daily ward rounds to enforce compliance on the usage of the pathway.
The many missing GPR associations (Invisible pathway) on the path leading from lysine to 2-oxoadipate, surely promote the usage of this specific pathway versus the alternative pathway leading from tryptophan to 2-oxoadipate, explaining the high contribution strength of AATAi (see Figure 5 and Table 1).
GEP has revealed three subtypes of aggressive lymphoma, discerning in developmental stage and usage of different oncogenic pathways.
Genome-wide molecular profiling has revealed these subtypes of aggressive lymphoma, with tumour cells arising from different lymphoid maturation stages and usage of different oncogenic pathways.
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