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The existence of the edge between two TFs indicates that the correlation between their activity profiles is above a threshold value of 0.70.
Subsequently, we can build a HB network for TFs, where a node is a TF and an edge between two TFs indicates they have similar HB profiles.
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The similarity of PPI partners between two TFs may suggest that they participate in the same regulatory mechanism.
We applied these design insights to generate a biosensor that tested and confirmed a predicted in vivo interaction between two TFs (ATF3 and Max), illustrating the potential for rationally-designed, TF-detecting biosensors as a routine analytical tool.
We developed a computational pipeline called TF-Cluster for identifying functionally coordinated TFs in two steps: (1) Construction of a shared coexpression connectivity matrix (SCCM), in which each entry represents the number of shared coexpressed genes between two TFs.
In this study, we developed a novel method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data.
In this paper, we developed a method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data.
We define the affinity co-occurrence between two TFs as the rank correlation between N T profiles of those TFs beyond what is explained by the similarity between pairs of PSAMs.
Sixty two of these tissue-type TF-TF interaction networks have a linear relationship between TFs with 1 to 4 internal TFs (i.e. TF connecting to 2 other TFs), indicating that the majority of the TF-TF regulatory networks have simple TF relationships for controlling tissue gene expression.
When osmotic or water stress were applied, both AtHB7 and AtHB12 transcripts levels were strongly induced, indicating that activation by these stress stimuli overcomes the feedback loops observed between these two TFs during plant growth and development.
These interaction forms include the activation or repression by a single TF, and the five interaction forms between any two TFs.
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