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As expected, most (5/8) of the components of the SYM signalling pathway passed the filter applied by Task4 (Additional file 5: Table S1), with the exception of DMI1/POLLUX and the nucleoporins NUP133, and NENA, which were known before to share close homologues with A. thaliana [ 28- 30].
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This dissociation pathway passes through a singlet transition state TS1/s with a barrier height of 40.64 kcal/mol and reaction energy of 34.58 above the initial reactant on the doublet potential energy surface.
Repeating this analysis using the standard definition of the p-value, we found that for the 70 gene list no pathway passes at any reasonable FDR, and even if we ignored the 70 gene list, still only the breast cancer estrogen signaling pathway was over represented in all the other three signatures tested.
In normal fibroblasts the canonical pathway passes through ALK5 which phosphorylates transcription factors Smad2 and 3.
According to Wang et al., the WNT signaling pathway passes signals to the Notch signaling pathway [ 48].
If the shortest path between most of the genes in the pathway passes through the node, Betweenness is high.
It is commonly presumed that the help-seeking pathway passes through several "filters", each of which exclude some help-seekers from the process [ 9, 10].
As this pathway passes through the external capsule, it is ventral and medial to the arcuate fasciculus/superior longitudinal fasciculus whose anatomical location is also shown in Fig. 5 for reference.
It would be interesting to investigate this hypothesis through ENM (and/or MD) computations that try to connect the phosphorylation site and the binding site of the kinase through a signaling pathway and test whether this pathway passes through the disease associated residues, as the computations presented here may suggest.
Note, for the sake of interpretation, 175 pathways passed our gene pathway size filter criteria (min = 15 probes; max = 250 probes).
In SPL, only a few overrepresented signal pathways passed the statistical criteria (q < 0.001), but overrepresentation of TLR pathway and Rac1 signaling in 0WexGF mice and apoptosis pathway signaling in 5WexGF mice was noted.
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CEO of Professional Science Editing for Scientists @ prosciediting.com