Using local gene expression similarities to discover regulatory binding site modules

BMC Bioinformatics

Table 2 Evaluation with experimental binding data

Previous studies	binding score
Segal et al. [26] Cell Cycle, 17 modules	0.588
Segal et al. [25] 48 modules	0.271
Beer at al. [24] 49 modules	0.286
Hvidsten et al. [4] Cell cycle 109 rules	0.538
Present method	binding score
corr. 0.6, 1316 rules	0.445 (0.776)
corr. 0.7, 807 rules	0.643 (0.844)
corr. 0.75, 643 rules	0.605 (0.850)
corr. 0.8, 487 rules	0.700 (0.879)

Comparison of binding scores (data from Harbison et al. [23]). For each method, the presented number represents the fraction of significant gene groups among all gene groups provided by that method (significance is defined as Bonferroni corrected p-value being below 0.01). For the present method, the results that score higher than all other studies are shown in bold. Correlation thresholds used in the present clustering procedure are shown in the left column. Numbers in parentheses denote scores obtained for all genes (i.e. both genes with or without expression profiles).

ISSN: 1471-2105