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In particular, Interaction-Identifier method identifies that Oct4 and Sox2 help each other to stabilize onto DNA and attract the RNAP.
We propose an Interaction-Identifier method to identify the candidate form of interaction among the TFs and RNA polymerase (RNAP) on the promoter of a target gene.
We first apply the Interaction-Identifier method to identify the regulatory model for Nanog, following the same procedure as we did for the synthetic data.
Table 8 Number of errors in the back conversions of InChI identifiers Method Non-identity Non-identity after stripped stereochemistry Inchi N/A 97 Molconvert 1559 601 Molconvert-direct 773 595.
However as an approximation, the Interaction-Identifier method is still useful to analyze the biophysical properties of known TFs.
In this paper we explored Interaction-Identifier method to infer the interaction patterns between multiple ESC regulators.
The Interaction-Identifier method follows recent efforts [ 12, 25, 26] to translate TF concentrations into the equilibrium probability of RNAP binding using thermodynamic models.
We previously described the Interaction-Identifier method for identification of the candidate form of interaction among TFs and RNAP on the promoter of a target gene [ 14].
The Network-Identifier method utilized a thermodynamic model for gene regulation to infer regulatory relationships from multiple time course gene expression datasets.
Chen et al [ 6] developed a Network-Identifier method untilizing a thermodynamic model to infer regulatory relationships from multiple time course gene expression datasets.
The Interaction-Identifier method should therefore be applicable to analyze a larger number of biological processes where steady state time course data are available.
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