On the other hand, some expected pathways as secologanin and isoflavonoids were not identified in I. indigotica transcriptome.
As expected, these pathways are mostly related to fatty acids metabolism pathways.
The effect of small molecules on their expected target pathways was determined by querying the small molecule-GO network in the network visualization software Cytoscape [ 69].
Unexpectedly, MEK/ERK and AKT signaling were elevated in the absence of TIEG1, which is the opposite of what one would expect if these pathways were causing the defect in osteoclast differentiation.
Clearly, the more interactors were shared, the more common pathways were expected.
Therefore, the carbon fluxes of the NADH-dependent pathways were expected to be triggered to decrease in the recombinant strain.
Although SCP impairment is attributable to cortical and/or subcortical damage, only post-receptoral visual pathways were expected to be affected and, in this case, a red-green, blue-yellow or general impairment.
Likewise to P-invariants, each T-invariant should enjoy a biological meaning, and – vice versa – there should not be an expected pathway without corresponding T-invariant.
As expected, we found that both pathways were active in control or P-scr transfected cells demonstrating the specificity of P-1257 inhibitinging the PI3K/Akt pathways.
An estimate of the FDR for the association between a small molecule and its expected biological pathway was computed as the proportion of small molecules that were also connected to that category in the network.
