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Alternatively, as the JASPAR motif library used does not include all COUP-TF motifs, it is possible that the predicted COUP-TFI sites actually represent regulation by another member of the family.
These responses could represent regulation by other transcription factors.
These fluxes are comparisons between adapted and naïve flies during hypoxia, and do not represent regulation from normoxia to hypoxia.
The overlapping high-level domains represent regulation of cell growth and proliferation, cell migration, immune response regulation, response to hormones, and angiogenesis regulation.
It is worth noting that PERs and CRYs do not possess DNA binding domains, but we still retain the data as we believe that they might represent regulation by a complex composed of these important circadian proteins.
In the metabolism category the highlighted terms represent regulation of metabolic process (GO 0019222), glucose metabolic process (GO 0006006), carotenoid and terpenoid biosynthetic process (GO 0016177, GO 00016114, respectively) and proline biosynthesis process (GO 0006561).
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There are other approaches to build RAs but we think that this is the first one that takes advantage of patterns to properly represent regulations.
As noted above, these most likely represent regulations which proceed via intermediate states and hence cannot be identified by seed sequence matches.
While largely disconnected, these ontologies can be connected by edges representing regulation relationships.
The proposed algorithm returns a directed graph of regulatory interactions between P genes in form of a weighted adjacency matrix V ∈ ℝ P × P, where v i, j represents regulation of gene j by gene i.
In a memorable 2003 incident, top bank regulators staged a photo-op in which they used garden shears and a chainsaw to cut up stacks of paper representing regulations.
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