Fig. 5 | Nature Communications

Fig. 5

From: Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

Fig. 5

Direct regulated transcription factor (TF) targets are enriched for cis-motif clusters of partner TFs. Heatmap of enriched consensus cis-motifs for the 80 cis-motif clusters (columns) in the 500 bp promoter of the a induced and b repressed direct regulated targets of the 33 nitrogen (N)-early response TFs. The consensus cis-motif (CCM) logo, cluster number, and family representation for each CCM is shown above. Instances where there is a validated interaction between the TF under study and another TF within a family represented by the enriched CCM cluster are marked by a black circle. Of the 33 TFs validated in TARGET, only TFs with enrichment of any of the 80 CCMs in the 500 bp promoter are shown. Cis-binding motif clusters were determined using cis-motifs for Arabidopsis transcription factors collected from DNA affinity purification sequencing (DAP-seq)5, Cis-BP38, and protein binding microarrays (PBM)39. Blue shading represents p values calculated using Fisher’s exact test and false discovery rate (FDR) corrected. Source data of Fig. 5a, b are provided as a Source Data file

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