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Genes are regulated by interactions with multiple functional TFs in metazoans [ 8].
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Although current software is well established and can find the TFBS of single TFs, annotation of multiple functional TFBSs using the same PTM remains challenging [ 23].
The most highly-ranked TFs identified through the analysis, p53, c-Jun, and c-Myc, were identified in multiple functional groups.
Nodes with multiple functional links represent "functional hubs".
Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions.
And we have expanded the number of functional TF-gene binding pairs by about 6 folds.
All in all, our method can extract functional TF-gene binding pairs with better expression coherence.
Hence we conclude that our method can distinguish functional TF-gene binding pairs from non-functional binding pairs.
Because gene regulation typically involves combinatorial action of multiple TFs, functional binding sites tend to occur as groups that are often referred to as cis-regulatory modules (CRMs) [29].
These results revealed not only the common mechanisms for transcriptional regulation but also the common functional role of multiple interacting TFs between cancer and immune systems, including cell cycle, cell division, DNA replication, mitosis, phosphoinositide-mediated signaling, and immune response.
The resulting number of co-functional TF pairs was 543.
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