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.

ChIP-chip

CM

FI_TM

Our_final

GRAM

MA-Networker

PPV (%)(lit; con_mot)

4.6; 32.7

6.0; 35.8

18.2; 24.5

13.6; 48

6.3; 24.6

6.5; 38.6

SNST (%)(lit; con_mot)

13.7; 40.2

4.2; 10.5

1.7; 0.9

2.0; 2.9

7.9; 12.8

6.9; 16.8

N_pairs

3598

857

110

177

1518

1272

N_genes

1837

393

44

66

655

989

N_TFs

95

24

30

18

69

36

Lee et al. BMC Bioinformatics 2008 9:32   doi:10.1186/1471-2105-9-32