PhosR

PhosR enables comprehensive processing and functional analysis of mass spectrometry-based phosphoproteomic data to infer active kinases and signaling pathways.

Key Features:

• Data Processing: PhosR provides filtering, imputation, and normalization of phosphoproteomics data using stably phosphorylated sites.
• Kinase Activity Inference: PhosR performs functional analysis to infer active kinases from phosphoproteomic datasets.
• Signalome Construction: PhosR implements a method for identifying signaling modules that summarize and visualize interactions of kinases and their collective actions on signal transduction.
• Signaling Pathway Analysis: PhosR enables inference of signaling pathways from phosphoproteomic data.

Scientific Applications:

• Phosphoproteomic Data Processing: PhosR facilitates imputation, normalization, and filtering of mass spectrometry-based phosphoproteomic datasets.
• Kinase Activity Profiling: PhosR enables inference of active kinases and their collective actions on signal transduction from global phosphorylation profiles.
• Signaling Module Identification: PhosR constructs signalomes to identify collections of signaling modules for summarizing kinase interactions and signal transduction.

Methodology:

PhosR implements data imputation and normalization using a set of stably phosphorylated sites, and constructs signalomes through a signalome construction method for identifying signaling modules.