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So what is the most upstream regulator?
One answer is that the most upstream regulator is epigenetic change.
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At the same time, broad variations in the levels of the most upstream regulators are unlikely to be compatible with life - therefore distribution of variation across the tiers of significance should be optimized, by maximized population survival.
To identify genes at the core of the tumor suppressor program, we decided to focus on direct transcriptional targets of TGF-β, reasoning that hierarchically these would be the most upstream regulators of the program.
CD40 and several proinflammatory cytokines e.g. IL-1b, TNFa and IL-8 were up-regulated in our dataset, and CD154 was predicted as the most significant upstream regulator (Table 5, Figure 4).
Bone morphogenetic protein 4 was the most significant upstream regulator (P overlap = 1.99 × 10−6).
In silico pathway analysis predicted that ATF4 was the most significant upstream regulator orchestrating pathological processes after ONC.
Peptidoglycan was identified as the most significant upstream regulator for the List eQG (Table 5, Figure 4).
IPA analysis identified the transforming growth factor (TGF β pathway as the most significant upstream regulator of the transcriptional network in preM ER+ breast cancer (Additional file 6).
Our study also revealed that GRP78 – an ER-resident protein – assisting in protein folding and the most important upstream regulator of the unfolded protein response due to ER-stress, was exclusively upregulated during MI along with the levels of proximal effectors of ER stress PERK, IRE1 and phospho IRE1.
IFNG, one of the most probable upstream regulators, is known for its paramount role in acute rejection.
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