motifeR

motifeR identifies and visualizes protein post-translational modification (PTM) motifs from mass spectrometry-derived proteomic datasets to support motif discovery and kinase signaling analysis.

Key Features:

• Motif Extraction and Visualization: Extracts statistically significant motifs from large PTM datasets and generates visual representations for interpretation.
• Multi-Modification Site Enrichment Analysis: Integrates functions for enrichment analysis of multi-modification sites.
• Inclusion of Low Location Probability Sites: Supports motif discovery that includes peptides with low location probability and potentially overlooked modification sites.
• Kinase Signaling Network Characterization: Estimates and models differential kinase signaling networks for human phosphoproteomics by integrating kinase–substrate relations from the NetworKIN database.
• Statistical Significance Assessment: Identifies motifs based on statistical criteria to ensure relevance in large-scale proteomic datasets.

Scientific Applications:

• PTM Motif Discovery: Enables identification and visualization of sequence motifs surrounding protein modification sites.
• Protein Function and Regulation Analysis: Supports investigations into how PTMs affect protein function and regulatory mechanisms.
• Kinase Signaling and Pathway Analysis: Facilitates characterization of kinase signaling networks and cellular signaling pathway studies using phosphoproteomics data.
• Disease Mechanism and Therapeutic Target Studies: Supports research into disease mechanisms and the identification of potential therapeutic targets through PTM and kinase-network analysis.

Methodology:

Uses algorithms for motif extraction with statistical significance assessment from proteomic datasets and integrates kinase–substrate relations from the NetworKIN database for kinase-network estimation.