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DOI: 10.14569/IJACSA.2020.0110213
PDF

Discovering the Relationship between Heat-Stress Gene Expression and Gene SNPs Features using Rough Set Theory

Author 1: Heba Zaki
Author 2: Mohammad Nassef
Author 3: Amr Ahmed Badr
Author 4: Ahmed Farouk Al-Sadek

International Journal of Advanced Computer Science and Applications(IJACSA), Volume 11 Issue 2, 2020.

  • Abstract and Keywords
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Abstract: Over the years of applying machine learning in bioinformatics, we have learned that scientists, working in many areas of life sciences, call for deeper knowledge of the modeled phenomenon than just the information used to classify the objects with a certain quality. As dynamic molecules of gene activities, transcriptome profiling by RNA sequencing (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Moreover, Single nucleotide polymorphisms (SNPs) are of great potential in genetics, breeding, ecological and evolutionary studies. Rough sets could be successfully employed to tackle various problems such as gene expression clustering and classification. This study provides general guidelines for accurate SNP discovery from RNA-seq data. Those SNPs annotations are used to find relation between their biological features and the differential expression of the genes to which those SNPs belong. Rough sets are utilized to define this kind of relationship into a finite set of rules. Set of (32) generated rules proved good results with strength, certainty and coverage evaluation terms. This strategy is applied to the analysis of SNPs in A. thaliana plant under heat-stress.

Keywords: RNA sequencing (RNA-seq); variant calling; Single Nucleotide Polymorphisms (SNPs) analysis; rough sets; gene expression

Heba Zaki, Mohammad Nassef, Amr Ahmed Badr and Ahmed Farouk Al-Sadek, “Discovering the Relationship between Heat-Stress Gene Expression and Gene SNPs Features using Rough Set Theory” International Journal of Advanced Computer Science and Applications(IJACSA), 11(2), 2020. http://dx.doi.org/10.14569/IJACSA.2020.0110213

@article{Zaki2020,
title = {Discovering the Relationship between Heat-Stress Gene Expression and Gene SNPs Features using Rough Set Theory},
journal = {International Journal of Advanced Computer Science and Applications},
doi = {10.14569/IJACSA.2020.0110213},
url = {http://dx.doi.org/10.14569/IJACSA.2020.0110213},
year = {2020},
publisher = {The Science and Information Organization},
volume = {11},
number = {2},
author = {Heba Zaki and Mohammad Nassef and Amr Ahmed Badr and Ahmed Farouk Al-Sadek}
}



Copyright Statement: This is an open access article licensed under a Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, even commercially as long as the original work is properly cited.

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