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Open Access Research

A statistical thin-tail test of predicting regulatory regions in the Drosophila genome

Jian-Jun Shu* and Yajing Li

Author Affiliations

School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore

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Theoretical Biology and Medical Modelling 2013, 10:11  doi:10.1186/1742-4682-10-11

Published: 14 February 2013

Abstract

Background

The identification of transcription factor binding sites (TFBSs) and cis-regulatory modules (CRMs) is a crucial step in studying gene expression, but the computational method attempting to distinguish CRMs from NCNRs still remains a challenging problem due to the limited knowledge of specific interactions involved.

Methods

The statistical properties of cis-regulatory modules (CRMs) are explored by estimating the similar-word set distribution with overrepresentation (Z-score). It is observed that CRMs tend to have a thin-tail Z-score distribution. A new statistical thin-tail test with two thinness coefficients is proposed to distinguish CRMs from non-coding non-regulatory regions (NCNRs).

Results

As compared with the existing fluffy-tail test, the first thinness coefficient is designed to reduce computational time, making the novel thin-tail test very suitable for long sequences and large database analysis in the post-genome time and the second one to improve the separation accuracy between CRMs and NCNRs. These two thinness coefficients may serve as valuable filtering indexes to predict CRMs experimentally.

Conclusions

The novel thin-tail test provides an efficient and effective means for distinguishing CRMs from NCNRs based on the specific statistical properties of CRMs and can guide future experiments aimed at finding new CRMs in the post-genome time.

Keywords:
Statistical approach; Transcription factor binding sites (TFBSs); Cis-regulatory modules (CRMs)