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A cross talk between codon usage bias in human oncogenes.

Tarikul Huda Mazumder1, Supriyo Chakraborty1, Prosenjit Paul1

  • 1Department of Biotechnology, Assam University, Silchar 788011, Assam, India.

Bioinformation
|June 27, 2014
PubMed
Summary
This summary is machine-generated.

Mutation pressure significantly influences oncogene codon usage, impacting gene expression. Highly expressed oncogenes exhibit high GC content and codon usage bias, revealing key evolutionary forces.

Keywords:
Codon usage patternOncogeneSynonymous codon

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Oncogenes are genes with the potential to induce cancer.
  • Codon usage bias provides insights into genome evolution.
  • Understanding these biases is crucial for cancer research.

Purpose of the Study:

  • To investigate the factors shaping codon usage patterns in oncogenes.
  • To determine the relationship between codon usage bias and oncogene expression levels.

Main Methods:

  • Analysis of gene expression using the codon adaptation index (CAI).
  • Assessment of GC content at different codon positions.
  • Correlation analysis using Spearman's rank correlation coefficient.

Main Results:

  • Moderate correlations observed between CAI and GC content.
  • Significant positive correlation between GC content at first/second codon positions and third codon position.
  • Strong negative correlation between ENC and GC3s values; positive correlation between CAI and ENC.

Conclusions:

  • Mutation pressure is the primary driver of oncogene codon usage patterns, outweighing natural selection.
  • Codon usage bias is a determinant of oncogene expression levels in humans.
  • Highly expressed oncogenes are characterized by high GC content and significant codon usage bias.