Table 1 Parameters used for prediction analysis and their properties
From: Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
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 |