Extended Data Figure 7: Heat map showing entire DEPICT gene set enrichment results.

This figure is analagous to Fig. 2. For any given square, the colour indicates how strongly the corresponding gene (shown on the x axis) is predicted to belong to the reconstituted gene set (y axis). This value is based on the Z score of the gene for gene set inclusion in DEPICT’s reconstituted gene sets, where red indicates a higher Z score and blue indicates a lower one. The proteoglycan-binding pathway was uniquely implicated by coding variants (as opposed to common variants) by both DEPICT and the Pascal method. To visually reduce redundancy and increase clarity, we chose one representative ‘meta-gene set’ for each group of highly correlated gene sets based on affinity propagation clustering (see Methods and Supplementary Information). Heat map intensity and DEPICT P values correspond to the most significantly enriched gene set within the meta-gene set; meta-gene sets are listed with their database source. Annotations for the genes indicate whether the gene has OMIM annotation as underlying a disorder of skeletal growth (black and grey) and the MAF of the significant ExomeChip variant (shades of blue; if multiple variants, the lowest-frequency variant was kept). Annotations for the gene sets indicate if the gene set was also found significant for ExomeChip by the Pascal method (yellow and grey) and if the gene set was found significant by DEPICT for ExomeChip only or for both ExomeChip and GWAS (purple and green). GO, Gene Ontology; KEGG, Kyoto encyclopaedia of genes and genomes; MP, mouse phenotype in the Mouse Genetics Initiative; PPI, protein–protein interaction in the InWeb database.