Fig. 5

A brain-specific TF-target gene regulatory network for AD. The TF-target gene network was generated by mapping the significant SNPs with AD from the PheWAS Catalog into the enhancer or promoter regions via three components: (1) genome-wide mapping of promoters and enhancers; (2) linking TFs to promoters and enhancers; and (3) linking enhancers and promoters to target genes as described in “Methods.” TFs are denoted by Vee and target genes with significant SNPs are denoted by circles. The node color is coded based on the brain-specific gene expression quantified by z-scores using the RNA-sequencing (RNA-seq) data from GTEx (see “Methods”). A larger z-score indicates a higher expression level in brain compared to other tissues. Green lines represent the enhancer-gene regulations and orange lines represent the promoter-gene regulations. Several TFs and targeted genes (e.g. ZIC1, STX1B, CDH13, and SKA2) described in the main text are highlighted. Both Figs. 5 and 6 were prepared using Cytoscape (v2.8.1)