On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence

Background: In eukaryotes, most DNA-binding proteins exert their action as members of large effector complexes. The presence of these complexes are revealed in high-throughput genome-wide assays by the co-occurrence of the binding sites of different complex components. Resampling tests are one route by which the statistical significance of apparent co-occurrence can be assessed. Results: We have investigated two resampling approaches for evaluating the statistical significance of binding-site co-occurrence. The permutation test approach was found to yield overly favourable p-values while the independent resampling approach had the opposite effect and is of little use in practical terms. We have developed a new, pragmatically-devised hybrid approach that, when applied to the experimental results of an Polycomb/Trithorax study, yielded p-values consistent with the findings of that study. We extended our investigations to the FL method developed by Haiminen et al, which derives its null ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: David S. Huen, Steven Russell
• Keywords: BMCBI 2010, Co-occurrence, Hybrid Method, Statistical Significance