Fig. 1.

Maize Gene Regulatory Networks (GRNs) in four tissues. a Number of RNA-Seq libraries used to build GRNs in each tissue. Libraries were grouped into tissues based on SRA metadata data and/or published papers (details in Supplemental table1). SAM: shoot apical meristem. b A Venn diagram showing the overlap of genes expressed in leaf, root, SAM and seed. A gene was designated as expressed in a tissue if it had counts per million (CPM) value higher than 1 in more than 10% of libraries. c An UpSet graph showing the overlap of expressed Transcription Factors (TFs) in each tissue. Number of TFs expressed in each individual or combination of tissues were represented in bar plot (orange). The intersections were represented by connected black dots. Total number of TFs expressed in each tissue were represented in blue bar plot. d Expression heatmap of 1409 TFs that were expressed in all four tissues. TFs were clustered into 15 sub-groups (separated by dashed lines) based on their expression patterns. Gene expression value from each tissue were averaged and z-transformed, resulting in a scaled expression values between − 1.5 and + 1.5 for each gene. Hierarchical Clustering was calculated by hclust() function in R