PhosX

PhosX estimates differential kinase activity from phosphoproteomics data by combining enrichment analysis statistics with kinases' substrate sequence specificity information.

Key Features:

• Data-driven kinase activity inference: Identifies upregulated and downregulated kinases without relying on manually curated kinase-substrate associations.
• Substrate sequence specificity integration: Exploits experimentally determined substrate sequence specificities of human kinases for activity estimation.
• Phosphopeptide-based analysis: Operates using only input phosphopeptides' sequences and intensity changes.
• Performance benchmarking: Outperforms currently available approaches for the same task and performs better or similarly to state-of-the-art methods that rely on previously known kinase-substrate associations.

Scientific Applications:

• Signalling mechanism elucidation: Points to causal mechanisms driving signalling processes through kinase activity inference.
• Drug target identification: Identifies potential drug targets by revealing differentially regulated kinases.
• Phosphoproteomics data analysis: Analyzes large phosphoproteomics datasets with known differentially regulated kinases.

Methodology:

PhosX combines state-of-the-art statistics in enrichment analysis with kinases' substrate sequence specificity information.