KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics

Area of Science:

• Biochemistry
• Bioinformatics
• Systems Biology

Background:

• Proteome-wide phosphoproteomics data is rapidly expanding for various model organisms.
• Understanding kinase-substrate interactions is crucial for deciphering cellular signaling pathways.

Purpose of the Study:

• To introduce KINAID (KINase Activity and Inference Dashboard), a novel computational tool.
• To enable prediction and visualization of kinase-substrate interactions across multiple species.

Main Methods:

• KINAID is an interactive web-based tool developed using Dash/Plotly.
• It analyzes phosphopeptide datasets to identify enriched kinases and cluster phosphopeptides.
• The tool supports data from Homo sapiens and 10 additional model organisms.

Main Results:

• KINAID successfully predicts kinase-substrate interactions.
• It identifies kinases targeted by enriched phosphopeptides.
• The tool interactively visualizes these interactions and clusters phosphopeptides.

Conclusions:

• KINAID is the first tool capable of analyzing kinase-substrate interactions across a wide range of model organisms.
• Its application to yeast phosphoproteomics data demonstrates its utility.
• KINAID facilitates the exploration of kinase activity and signaling networks.