Codonome

Codonome computes transcriptome-level codon frequencies by calculating "codonome value"—the total count of each specific codon across expressed mRNAs in a condition—and integrating codon bias with gene expression to estimate codonome bias.

Key Features:

• Codon Bias Calculation: Quantifies the differential frequency of synonymous codons (codon bias) in a given biological context.
• Integration with Gene Expression Data: Imports mRNA expression data from various sources in tabulated text format and integrates these expression levels with codon counts.
• Estimation of Codonome Bias: Combines codon bias and gene expression profiles to estimate the frequency of each codon across tissues or conditions (codonome bias).
• Cross-Species Analysis: Enables systematic comparison across human tissues and multiple species to assess evolutionary and functional aspects of codon usage.

Scientific Applications:

• Tissue-Specific Analysis: Explores how codon usage varies across human tissues to inform tissue-specific gene regulation studies.
• Comparative Genomics: Supports cross-species comparisons to identify conserved patterns of codon usage and their evolutionary significance.
• Disease Research: Investigates whether genetic anomalies and conditions such as aneuploidy and Down Syndrome-related acute megakaryoblastic leukemia (DS-AMKL) affect codon usage patterns.

Methodology:

Counts total mRNA codon numbers per organism and integrates these counts with tabulated gene expression data to derive transcriptome-level codon frequencies.