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Pathfinding algorithms often optimize for pathways with the smallest number of enzymatic steps, as these pathways tend to require less manipulation in a metabolic engineering context (Fig. 2b).
We found that true signalling pathways tend to involve more microRNAs and contain more interactions, as well as having more high degree nodes (degree ≥4) than pathways created out of a random set of starting nodes.
Following the observation that genes that function in biochemical pathways tend to be coordinately expressed, we hypothesized that the unique and predominantly expressed genes for each step are those that function in photorespiration.
The specific intricacies of each ligand notwithstanding, the differential activation is manifest as a differential kinetics of activation, as MyD88/Mal-dependent versus TRIF/TRAM-dependent pathways tend to proceed quickly from the plasma membrane and delayed from the endosome, respectively.
These critical pathways tend to run in parallel.
DEGs resulting from a specific perturbation to corresponding pathways tend to share some functional or physiological characteristics.
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Generally, we observed that functionally interacting pathways tended to exhibit similar deregulated expression patterns.
Related metabolic pathways tended to be organized toward the center rather than in the periphery at day 12 (Fig. 5d).
Thus, coincident activity of converging afferent pathways tends to switch the pathways to be LTP only or LTP/LTD depending on the activity states of the hippocampus.
Finally, tumors with greater CC+, anti-apoptosis and angiogenic pathways as well as lower Notch and complement pathways tended to have a greater proportion of the solid component.
Most genes related to over-represented metabolic pathways tended to be down-regulated at 36 h.
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