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A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis

Overview of attention for article published in Journal of Theoretical Biology, January 2015
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Title
A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis
Published in
Journal of Theoretical Biology, January 2015
DOI 10.1016/j.jtbi.2014.09.038
Pubmed ID
Authors

Roohollah Shamloo-Dashtpagerdi, Hooman Razi, Massumeh Aliakbari, Angelica Lindlöf, Mahdi Ebrahimi, Esmaeil Ebrahimie

Abstract

Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2×2) and Fisher's exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between the promoters. The results of the pairwise comparative analysis together with the expression data for the studied genes revealed the biological significance of the identified CREs.

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Mendeley readers

The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 1 3%
Sri Lanka 1 3%
Unknown 30 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 28%
Student > Master 6 19%
Researcher 5 16%
Student > Doctoral Student 2 6%
Other 2 6%
Other 5 16%
Unknown 3 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 53%
Biochemistry, Genetics and Molecular Biology 4 13%
Engineering 3 9%
Computer Science 2 6%
Social Sciences 1 3%
Other 1 3%
Unknown 4 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 12 August 2015.
All research outputs
#13,221,851
of 16,639,069 outputs
Outputs from Journal of Theoretical Biology
#2,562
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Outputs of similar age
#146,432
of 215,180 outputs
Outputs of similar age from Journal of Theoretical Biology
#47
of 76 outputs
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