NetCrafter Ontology-derived Gene Network Modeling, Visualization & Functional Interpretation

Latest update: June 2025

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NetCrafter is free to use

NetCrafter is an intuitive platform for constructing functional gene networks using biological ontologies and curated knowledgebases. It enables users to build biologically meaningful networks from either a simple list of genes or from genes combined with omics data - without relying on prior geneโ€“gene interaction data.

NetCrafter quantifies shared biological functions among genes using resources such as the Gene Ontology (GO), Human Phenotype Ontology (HPO), Hallmark genesets and Oncogenic Signature collections, allowing users to contextualize their results within well-established functional and disease-related frameworks.

>> See details of NetCrafter ontologies

This ontology-based scoring enables the creation of networks that reflect functional similarity and highlight key gene clusters (hotspots) related to biological pathways or disease phenotypes.

In addition, NetCrafter offers interactive ontology clustering and supports the integration of multiple datasets, making it a powerful tool for exploring gene functions, interpreting omics data, and identifying potential biomarkers or therapeutic targets.


      Gene networks

      Ontology clustering
Creating ontology-based gene networks

The figure illustrates the process of generating networks using Gene Ontology Biological Process (GOBP) terms and Human Phenotype Ontology (HPO) terms containing 3 to 300 genes.

For a gene list, the -log(p-value) of each ontology term was calculated using Fisherโ€™s exact test. ๐‘‡๐‘ค(๐บ1,๐บ2) denotes the p-value weighted Tanimoto score.

Ontolgoy clustering

Input ontology terms were clustered using the regular Tanimoto index between terms, ๐‘‡(๐‘‚1,๐‘‚2), which measures the overlap in shared genes.

Reference (Please cite the following paper when publishing your work using NetCrafter )
- NetCrafter: Ontology-based gene network construction and interpretation, submitted, 2025