Additional file 5: Figure S3. of CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

Relationship between the p value threshold for SNP inclusion and the number of significant trait pairs discovered by CPAG. Increasing the stringency of the p value threshold from 10−5 to 10−20 decreases the number of SNPs included in the CPAG analysis from 11,284 to 813. A similar number of statistically significant trait pairs is detected for a threshold of 10−5 to 10−8, but there was a decline in the number of significant pairs as the p value threshold was decreased to result in fewer included SNPs. Therefore, the detection of statistically significant pairs is robust against increasing false positive SNPs as the p value threshold is made less stringent, while making the p value threshold increasingly stringent decreases the discovery of significant trait pairs. (PDF 354 kb