TEKRABber

TEKRABber estimates correlations of orthologs and transposable elements between two species by normalizing expression counts using orthology confidence from BioMart and detecting differentially expressed orthologs and TEs.

Key Features:

• Orthology-aware normalization: Uses orthology confidence between two species from BioMart to normalize expression counts.
• Differential expression analysis: Detects differentially expressed orthologs and transposable elements.
• Correlation analysis: Performs one-to-one correlation analysis for desired orthologs and transposable elements.
• RNA-seq data compatibility: Accepts user-prepared ortholog and transposable element RNA-seq expression data following specified data structures.

Scientific Applications:

• Cross-species comparative genomics: Compares orthologs and transposable elements between two species to identify evolutionary patterns.
• Regulatory network analysis: Analyzes interactions between KRAB-ZNF genes and transposable elements in primate brain evolution and disease.
• Brain evolution research: Investigates species-specific interactions, such as human-specific KRAB-ZNF and transposable element relationships.
• Disease association studies: Examines altered regulatory networks, such as diminished KRAB-ZNF and Alu interactions in Alzheimer's disease.

Methodology:

TEKRABber uses orthology confidence data from BioMart to normalize expression counts, followed by differential expression detection and one-to-one correlation analysis between orthologs and transposable elements.