Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia
Figure 2
(A) Circos plots integrating the Global Test and FORGE analysis and heatmaps for the levels of single nucleotide polymorphism (SNP)- and gene significance.
(B) Inset legend providing information represented by each data ring. Notes: for visibility, the implicated gene locations were zoomed in upon by up to 1200%. The inset legend image provides information represented by each ideogram. −log10 of the individual SNP and the gene p-values increase radially outward. The arc of each heatmap wedge maps directly to the location of the SNP in the genome. The arc width is proportional to the size of the associated gene (plus 20 kb upstream and downstream). Individual SNP p-values for the BOMA-UTR and the GAIN-MGS data sets are shown as scatterplots on ideograms A and B. The gene p-values for Psychiatric Genetics Consortium (PGC) datasets are shown as a scatterplot on ideogram C. The significance scores for genes contributing to a pathway significance are shown as heatmaps on ideograms 1–14. 1 - dbGO:0050808:synapse organization; 2 - dbKEGG:04514:cell adhesion molecules; 3 - dbCGP:Kyng dna damage by UV; 4 - dbKEGG:04210:apoptosis; 5 - dbGO:0046914:transition metal ion binding; 6 - dbGO:0008270:zinc ion binding; 7 - dbGO:0010628:positive regulation of gene expression; 8 - dbMIR:gagcctg,mir-484; 9 - dbTFT:v$cebpa 01; 10 - dbTFT::v$hnf4 q6; 11 - dbTFT:v$chop 01; 12 - dbTFT:v$ptf1bea q6; 13 - dbTFT:v$ciz 01; 14 - dbTFT:v$sox5 01. The darker the red, the higher the contribution of the SNP/gene to the association of the respective pathway. Comparing the overlapping of important genes in different pathways allows investigation of whether they lie within intersections of those pathways.