even for weak functional associations. Thousands of genes are meaningfully coexpressed for one cellular function (15). However, this long-range characteristic becomes problematic when a researcher wants to search for only directly associated genes, as in protein–protein interaction relationships. To focus on searching for directly associated genes with functions that can be successively examined by experiments, such as for protein binding or for gene disruption/overexpression, there are two fundamental refinement points for gene coexpression. The first point is the construction of more reliable, high-quality coexpression data, and the second point is the accurate estimation of the quality of the coexpression data. In addition, an appropriate data representation framework is valuable to distinguish true gene associations from false ones. Even if the average predictive performance is low, appropriate data representation with accurate reliability scores for each prediction will safely guide users to select the appropriate genes to design new experiments.
