About the Molecular AOP Analyser

The Molecular AOP Analyser is a web-based tool for Key Event enrichment analysis of transcriptomic data in the context of Adverse Outcome Pathways. It enables researchers and regulators to statistically assess which Key Events within an AOP are supported by their experimental gene expression data.

Purpose

Given a differential gene expression dataset and a selected AOP, the tool tests which Key Events' gene sets respond in your data. Two methods are offered: Fisher's exact test, a threshold-based over-representation test, and GSEA, a threshold-free ranking method that is direction-aware. Both report Benjamini–Hochberg-adjusted results, and both distinguish Key Events that are over-represented from those that are depleted. Results are visualised as an interactive AOP network with gene-level expression colouring, and on the underlying WikiPathways diagrams.

Part of VHP4Safety

This tool is developed as part of the VHP4Safety (Virtual Human Platform for Safety Assessment) project, an initiative to develop a virtual human platform for next-generation risk assessment of chemicals, pharmaceuticals, and other substances.

Data Sources

Key Event gene set mappings are curated in the molAOP Builder, which links AOP Key Events to three resources you can select between: WikiPathways, Gene Ontology (Biological Process) and Reactome. Every mapping carries a curator-assigned confidence level, which you can use as a filter. AOP structure — Key Events and their relationships — comes from the AOP-Wiki RDF endpoint.

How to cite

An enrichment result rests on the curated mappings as much as on this software, and the two carry separate DOIs:

• This software: 10.5281/zenodo.21914317 (concept DOI — always the newest release; cite the version DOI of the release you used if the result must be reproducible)
• The KE→pathway mappings: the molAOP Builder dataset, 10.5281/zenodo.20184643
• The Builder application, if you curated mappings with it: 10.5281/zenodo.21914244

Please also cite the underlying resources you selected (AOP-Wiki, WikiPathways, Gene Ontology, Reactome). Machine-readable metadata is in CITATION.cff.

Source and licence

Source code: github.com/marvinm2/molAOP-analyser, released under GPL-2.0-only. The running version and build are reported at /health.

Contact

For questions, feedback, or collaboration enquiries, please contact the VHP4Safety bioinformatics team or visit the VHP4Safety website.