title: A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis.
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.
authors.affiliation: Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran.
authors.forename: Roohollah
authors.initials: R
authors.lastname: Shamloo-Dashtpagerdi
authors.affiliation: Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran. Electronic address: razi@shirazu.ac.ir.
authors.forename: Hooman
authors.initials: H
authors.lastname: Razi
authors.affiliation: Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran.
authors.forename: Massumeh
authors.initials: M
authors.lastname: Aliakbari
authors.affiliation: Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden.
authors.forename: Angelica
authors.initials: A
authors.lastname: Lindlöf
authors.affiliation: Alumnus from Saarland University, Department of Informatics, Saarbrucken, Germany.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Ebrahimi
authors.affiliation: Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran; Discipline of Genetics, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia. Electronic address: esmaeil.ebrahimie@adelaide.edu.au.
authors.forename: Esmaeil
authors.initials: E
authors.lastname: Ebrahimie
mesh_terms: D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics; D015233:Models, Statistical; D016012:Poisson Distribution; D011336:Probability; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D012045:Regulatory Sequences, Nucleic Acid
keywords: CREs occurrence; Motif enrichment; Transcriptional regulation