We applied GPA to analyze the bladder cancer GWAS -values with one annotation dataset at a time, and performed hypothesis testing to assess the significance of enrichment. The results are shown in the left panel of Figure 8. Under significance level after Bonferroni correction, annotations from 19 cell lines were statistically significantly enriched for bladder cancer risk associated SNPs. Most of these cell lines were derived from lymphocytes from normal blood (e.g., T cells CD4+ Th0 adult, Monocytes CD14+ RO01746), while some cell lines came from cancer patients (e.g., Gliobla and HeLa-S3). The above results suggest that involvement of the immune system and carcinoma pathways in bladder cancer. These results also demonstrate that GPA may be an effective way to explore functional roles of GWAS hits by testing enrichment on phenotype-related annotations or user-specified annotations.
