Table 1.

Parameters used for prediction analysis and their properties

Parameter	Information it gives	Drawback
Total = Frequency of gene pair co-expression	Total number of times a gene pair is expressed, excluding missing values	Some genes are expressed more frequently than others
MIM = Mutual Information Measure	Specificity of co-expression	When Total is small, MIM can be artificially high
R2 = Pearson’s Correlation Coefficient	Correlation between gene pair expression levels	Will detect global, but not conditional, co-regulation. Also, non-expression is far more common than expression, biasing R2 (e.g., 2 genes never expressed will show perfect correlation)
P = Purity	When co-expression “behavior” is described in terms of discrete categories, purity reflects a relative breakdown of behavioral observations	Information can be lost when discretizing a continuous variable