Identifying Driver Potential in Passenger Genes Using Chemical Properties of Mutated and Surrounding Amino Acids

Das, Jayanta Kumar; Choudhury, Pabitra Pal; Roy, Bidyut

doi:10.1007/978-981-13-0544-3_10

Cited by 1 publication

(2 citation statements)

References 18 publications

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“…To study the same, quantitatively we consider the major three types of codon classes (Strong, Transitional and Weak) transitions from wild type to disease or mutated. The density of each codon is deducted from the density of nucleotides, where the density of C = 1.55 g/cm 3 , G = 2.2 g/cm 3 , T = 1.32 g/cm 3 and A = 1.60 g/cm 3 . Hence, the density of a codon is the average densities of the constituent nucleotides of the codon.…”

Section: Alteration Of Physical Density Of Codon With the Change In Codon Groupmentioning

confidence: 99%

“…For example, T T T ⇒ T T C change ultimately has no effect on protein as both the codons code for the amino acid Phenylalanine. A missense mutation refers to a base substitution where alteration in any nucleotide bases alters the amino acid [3,4]. For instance, ACA ⇒ AAA alteration causes the alteration in coded amino acid from Threonine to Lysine.…”

Section: Introductionmentioning

confidence: 99%

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Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

Sengupta¹,

Choudhury

Chakraborty

et al. 2020

Preprint

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Motivation: Alteration of amino acid is possible due to mutation in codons that could have a potential impact in a diseased condition. Effective mutation analysis can help to predict the fate of the diseased individual which can be validated later by in-vitro experimentations. It may also help an individual who is asymptomatic but having a particular genetic change for early detection and diagnosis during any terminal diseases. We try to investigate the codon alteration patterns and its impact during mutation for the genes known to be responsible for a particular disease.Results: For our current study, we consider neurodegenerative and monogenic diseases. We use numerical representation based on a determinative degree and classification of codons as well as amino acids into three different classes (Strong, Weak and Transition) for the analysis. Our analysis reveals that the strong class codons are highly mutated followed by weak and transition class. We observe that most of the mutations occur in the first or second positions in the codon rather than the third. While looking into the chemical properties of amino acid, we observe that amino acids belong to the aliphatic group are affected most during missense mutations. Our investigation further emphasises that in most of the cases the change in the determinative degree of codon due to mutation is directly proportional to the physical density property. In addition, our scheme gives a more microscopic and alternative representation of the existing codon table that helps in deciphering interesting codon alteration patterns during mutations in disease pathogenesis.

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Section: Alteration Of Physical Density Of Codon With the Change In Codon Groupmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

Sengupta¹,

Choudhury

Chakraborty

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Identifying Driver Potential in Passenger Genes Using Chemical Properties of Mutated and Surrounding Amino Acids

Cited by 1 publication

References 18 publications

Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

Investigation of Codon Alternation Patterns in Genetic Diseases through Numerical Representation and Codon Classification

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