Fig. 5

Construction of a transcription factor regulatory network. A To build network, an edge was created when a motif binding site of a source TF overlapped DHSs and locate in a target TF gene, including 1500 bp upstream of the target TF’s transcription start site. For example, TF A and TF B regulate TF X, while TF X controls gene 1, gene 2, and gene 3. In order to increase the credibility of the transcription factor regulatory network, the co-expressed regulatory network was generated and merged with DNase-seq network to obtain the final regulatory network. B Changes in regulation patterns during ovule and fiber development in outgoing and incoming connections. Outgoing connections represent the number of genes regulated by this TFs. Incoming connections represent the number of TFs regulate this TFs or genes. C, D Overview of DNase-seq tracks for representative TF interactions in cotton TF regulatory network. The TCP14 recognition motif “GTGGGNCCCAC” (large coded) was identified from the upstream DHSs of GH_D11G0345. The CDC5 recognition motif “CTCAGC” (large coded) was identified from the upstream DHSs of GhMYB25. To the left of DNase-seq tracks is the subnetwork where GhMYB25 and GhTCP14. Diamonds represent TFs and rectangles represent genes. Dotted box indicates DHS regions, black line indicates CDC5 and GhTCP14 binding site. E Identification of hub TFs in TF network. Top 10 TFs were identified by cytoHubba. F Subnetworks of stress-related NAC2. Diamonds represent TFs and rectangles represent genes