Figure 4.
Transcriptional regulatory network diagram of cGMP upregulated genes generated by promoter analysis in order to predict A. thaliana co-expressed genes. The 59 upregulated gene promoters of a length 2,200 nt covering 2,000 nt upstream and 200 nt downstream of the 5′ end of the respective genes. The data was created with the Dragon Motif Builder (apps.sanbi.ac.za/MotifBuilder/index.php)32 and displayed with Cytoscape. (Dragon Motif Builder parameters: Algorithm EM2, motif length 9, threshold 0.9, no background, number of motif families = 30). The red dot denotes a hub gene (AtCHX8) and signifies the cGMP upregulated gene that shares the highest number of common promoter motifs with other A. thaliana genes. The green dot indicates At5G36240, a zinc knuckle (CCHC-type) family protein which contains the highest number of shared motifs per edge. At5g38480 general regulatory factor, a 14-3-3 gene, is represented by the blue dot on the figure. This gene is only linked to one gene and thus shares notable common motifs with a single gene only.