iProPhos

iProPhos performs integrated analysis of mass spectrometry-based proteomics and phosphoproteomics data to support comparative, differential, correlation, and enrichment analyses including kinase–substrate relationships.

Key Features:

• Extensive dataset integration: Integrates CPTAC-derived datasets comprising 1444 tumor samples and 746 normal samples across 12 cancer types for comparative analyses.
• Support for user-provided data: Accepts external proteomics and phosphoproteomics datasets for analysis alongside integrated repositories.
• Profiling and differential expression: Generates profiling plots and performs differential expression analysis for proteins and phosphosites.
• Survival and clinical association analyses: Conducts survival analysis and associates proteomic/phosphoproteomic measurements with clinical features.
• Correlation analyses: Performs correlation analyses including protein–protein, mRNA–protein, and kinase–substrate relationships.
• Functional and network enrichment analyses: Executes functional enrichment analysis, protein–protein interaction network analysis, and kinase–substrate enrichment analysis.

Scientific Applications:

• Cancer research: Supports identification of potential drug targets and upstream kinases involved in site-specific phosphorylation events using proteomics and phosphoproteomics data.
• Translational oncology and proteogenomics: Enables discovery of therapeutic targets and biomarker candidates from large-scale proteomics datasets.

Methodology:

Integration of CPTAC mass spectrometry proteomics and phosphoproteomics datasets (1444 tumor, 746 normal samples across 12 cancer types) with computational analyses including profiling plotting, differential expression, survival and clinical association analysis, correlation analyses (protein–protein, mRNA–protein, kinase–substrate), functional enrichment, protein–protein interaction network analysis, and kinase–substrate enrichment analysis.