Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Stat Appl Genet Mol Biol. 2010;9:Article29. doi: 10.2202/1544-6115.1434. Epub 2010 Aug 6.

Generalizing moving averages for tiling arrays using combined p-value statistics.

Author information

  • 1University of Colorado Denver, CO, USA. katerina.kechris@ucdenver.edu

Abstract

High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.

PMID:
20812907
[PubMed - indexed for MEDLINE]
PMCID:
PMC2942027
Free PMC Article

Images from this publication.See all images (6)Free text

Figure 1:
Figure 2:
Figure 3:
Figure 4:
Figure 5:
Figure 6:
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for iFactory Icon for PubMed Central
    Loading ...
    Write to the Help Desk