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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

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