Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

Table 4 Inputs and outputs of the proposed three-step approach

Steps	Inputs	Output(s)	Figure
Cluster genes into biologically relevant groups	- Gene expression profiles	Cluster centers/metagenes	Fig. 6
	- GO category information
Categorize TFs into different NMs	Gene expression profile of a TF	Predicted NM(s) for the TF	Fig. 7
	- Encoded binding site sequences for the TF
Infer NM-based TF-target relationship via RNN	- Gene expression profile of a TF	Identified cluster centers in the known or predicted NMs (i.e., identified TF-target gene relationship).	Fig. 8
	- Gene expression profiles of cluster centers (metagenes)
	- Known or predicted NM(s) of the TF

ISSN: 1471-2105