and the same gene in the case of different platform comparisons in the same species) in the top i genes in listr. To take into account different number of genes for each platform, we have modified k in the F1 from 100 to the top 1% of all genes in listg. To select the best reference guide gene, we checked all possible reference guide genes. The reference guide gene set R is composed of all available orthologous genes for different species. When multiple platforms are available for the species including the guide gene g, the same gene in the other platforms is also included in the reference guide gene set R. The COXSIM values are calculated between the target guide gene g and every reference gene r in R. The reference gene that gives the maximum COXSIM value is regarded as the best reference guide gene: (2)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}\begin{equation*} {{\it maxCOXSIM}_{1\% }^g} = \max _{r \in R} \left[ {{\rm COXSIM_{1\% }^g} (r)} \right] \end{equation*}\end{document}To assess statistical significance, the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{\it maxCOXSIM}_{1\% }^g}$\end{document} value is compared with the null distribution generated under the same
