Distribution of RNA 5-mers in Epigenetic Modification Regions and Genes Interactions

Document Type : Research Paper

Authors

1 Department of Computer Engineering, Faculty of engineering, Zanjan University,Zanjan, Iran

2 Department of Computer Engineering, Faculty of Engineering, Zanjan University, Zanjan, Iran

3 Department of Algorithms and Computation, Faculty of Engineering Science, College of Engineering, University of Tehran

10.22059/jac.2022.91076

Abstract

The demand for extracting sophisticated features, capable of effectively predicting gene interaction networks, from DNA or RNA sequences has increased in computational biology. The epigenetic modifications along with their patterns have been intensely recognized as appealing features affecting gene interaction. However, studying sequenced-based features highly correlated to this key element has remained limited. In this paper, the classification of 23 genes in the PPAR signaling pathway associated with muscle fat tissue in humans was proposed based on statistical distributions of the specified RNA-5-mers abundance. Then, we suggested that these 5-mers highly correlated to epigenetic modifications can efficiently categorize the different gene interactions, particularly co-expression interaction and physical interaction. Our results were evaluated according to GeneMania web interface shows that the geometric distribution of 5 mers in the epigenetic modifications region indicates the proportion of most physical interactions and the Poisson distribution the proportion of most Co-expression between genes
 

Keywords

Journal of Algorithms and Computation
Volume 54, Issue 2
December 2022
Pages 143-162

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