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. 2013 Feb 14:10:11.
doi: 10.1186/1742-4682-10-11.

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

Jian-Jun Shu  1 , Yajing Li
Affiliations

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

Jian-Jun Shu et al. Theor Biol Med Model. .

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.

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Figures

Figure 1
Figure 1
A flow chart of thin-tail test.
Figure 2
Figure 2
Histogram of CRMs (m = 5, j = 1, k = -0.3).
Figure 3
Figure 3
Histogram of CRMs (m = 5, j = 1, k = -0.14) after random shuffle.
Figure 4
Figure 4
Histogram of NCNRs (m = 5, j = 1, k = 0.54).
Figure 5
Figure 5
Histogram of NCNRs (m = 5, j = 1, k = 0.15) after random shuffle.
Figure 6
Figure 6
Histograms for CRMs and NCNRs classified by E (m = 5, j = 1).
Figure 7
Figure 7
Histograms for CRMs and NCNRs classified by T50(m = 5, j = 1).
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