Skip to main content

Table 1 Parameters used for prediction analysis and their properties

From: Predicting gene ontology from a global meta-analysis of 1-color microarray experiments


Information it gives


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