Table 1 Comparison of performance measures. For evaluation of our method, we compared our predicted TF-gene functional pairs (fourth column in bold, 'Our_final') with ChIP-chip results with annotated genes only (first column, 'ChIP-chip'), two prescription steps of our method (second and third columns, 'CM' and 'FI_TM'), and two other previous algorithms (fifth and sixth columns, 'GRAM' and 'MA-Networker'). Two performance measures were calculated, PPV and SNST for two reference datasets (see Methods). CM = all TF-gene pairs from coherent modules; FI_TM = TF-gene pairs from functional intersection among the initial putative transcriptional modules from ChIP-chip; lit = literature reference; con_mot = conserved motif reference; N_pairs = number of TF-gene pairs; N_genes = number of genes in the pairs; N_TFs = number of TFs in the pairs. Further comparison analysis is performed in Additional file 1. See the main text for details.

From: Prioritization of gene regulatory interactions from large-scale modules in yeast