Rtpca

Rtpca infers protein-protein interactions (PPIs) from thermal proteome profiling (TPP) data using thermal proximity coaggregation to analyze protein complex assembly and differential PPIs across conditions.

Key Features:

• Thermal proximity coaggregation analysis: Uses the thermal proximity coaggregation method to identify potential PPIs by comparing protein aggregation patterns across temperatures.
• Single-condition and differential analysis: Supports analysis of TPP datasets from both single-condition experiments and differential comparisons between conditions.
• Aggregation-pattern-based inference: Infers PPIs from changes in protein aggregation or thermal stability as a function of temperature.
• Integration with the R ecosystem: Interfaces with other R packages to enable incorporation into R-based analytical workflows.

Scientific Applications:

• Protein complex analysis: Characterize protein complex formation and assembly dynamics using TPP-derived aggregation profiles.
• Condition-specific PPI discovery: Detect differential or condition-specific interactions relevant to disease progression or response to treatment.
• Network modeling and target discovery: Provide inputs for predictive modeling of protein interaction networks to aid identification of novel therapeutic targets.

Methodology:

Analyzes TPP data by measuring changes in protein aggregation or thermal stability across temperatures using the thermal proximity coaggregation approach to infer PPIs.