Figure 3

Conceptual pipeline for TF→target predictions based on correlation and/or CRE analysis: Performed on All Expressed Genes. The strategy for determining TF→target interactions using both correlation analysis and CRE detection methods, using all expressed genes with a "Present call on the Affymetrix ATH1 microarray chip using the methodology previously described (see Figure 1). The analysis was reduced to using the Spearman correlation (which was previously shown to be the have more balanced performance compared to other correlation methods (based on the F measure)) alone or combined with CRE detection methods in order to determine changes in performance for these measures over the entire genome. TFs = Transcription Factors