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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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KeyPathwayMinerWeb: online multi-omics network enrichment.

Markus List¹, Nicolas Alcaraz², Martin Dissing-Hansen³

¹Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

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Summary

This summary is machine-generated.

KeyPathwayMinerWeb is a new online tool for pathway enrichment analysis. It identifies biological pathways from interaction networks and OMICS data, aiding biological discovery.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Pathway enrichment analysis is crucial for interpreting OMICS data.
Existing tools often require local installation and complex setup.
De novo network analysis can reveal novel biological insights.

Purpose of the Study:

To introduce KeyPathwayMinerWeb, an online platform for de novo pathway enrichment analysis.
To provide a user-friendly interface for integrating biological networks and OMICS data.
To enable seamless integration of network enrichment functionalities into other platforms via a RESTful API.

Main Methods:

Utilizes KeyPathwayMiner algorithms for extracting significant sub-networks.
Integrates biological interaction networks (e.g., protein-protein interactions) with molecular profiles (e.g., gene expression).
Offers batch processing for parameter optimization and visualization of extracted pathways.

Main Results:

KeyPathwayMinerWeb provides direct, browser-based de novo pathway enrichment analysis.
The platform successfully extracts connected sub-networks enriched with active or differentially regulated molecules.
A RESTful API is available for programmatic integration into other web services.

Conclusions:

KeyPathwayMinerWeb offers a novel, accessible solution for pathway enrichment analysis.
The tool facilitates the discovery of biologically relevant pathways from integrated network and OMICS data.
The availability of a RESTful API promotes broader adoption and integration within the bioinformatics community.