To test the enrichment of TD statistics in functional annotations, we allocated the cis-eQTLs to the 14 functional categories described above by physical position, and calculated the mean TD of each category. We assessed the enrichment using the inflation factor λ =\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\frac{{\bar T_{{\mathrm{D}}(i)}}}{{\bar T_{\mathrm{D}}}}$$\end{document}T¯D(i)T¯D, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\bar T_{{\mathrm{D}}(i)}$$\end{document}T¯D(i) is the mean TD of the cis-eQTLs in a category i, and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\bar T_{\mathrm{D}}$$\end{document}T¯D is the mean TD of all the cis-eQTLs. We then used the Jackknife approach (leaving one gene out at a time) described above to compute the variability of λ. Note that although we described the enrichment test method above based on cis-eQTLs, the method can be applied to data from genetic studies of different types of molecular phenotypes (e.g., DNAm and histone modification).
