To overcome these problems, we partially updated the quality measure. Instead to compare the top three coexpression edges, we compared two coexpressed gene lists, namely, the coexpressed gene list from a guide gene g of interest (listg) and that from a reference guide gene r (listr), which is the orthologous gene (or the same gene in the same species) in other platforms. To quantify the concordance of the two lists in a weighted manner, we introduced the measure COXSIM (8,20): (1)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}\begin{equation*} {\rm COXSIM}_{k}^{g}(r)= \sum \nolimits _{i=1}^{k} n(i, list_{g}, list_{r})/\sum \nolimits _{i=1}^{k} i, \end{equation*}\end{document}where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$n(i,list_g ,list_r )$\end{document} is the number of genes in the top i genes in listg having corresponding genes (orthologous genes in the case of different species comparisons, 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
