NetCrafter: Ontology-based gene network construction & interpretation

NetCrafter is an intuitive, user-friendly tool for creating gene networks and performing ontology clustering.

Users can easily generate gene networks by providing a gene list—without requiring additional gene–gene relationship data.

NetCrafter leverages ontologies such as Gene Ontology (GO) and Human Phenotype Ontology (HPO) to construct network structures specific to the input gene set.

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 Fisher’s exact test. 𝑇𝑤(𝐺1,𝐺2) denotes the p-value weighted Tanimoto score.

Ontolgoy clustering

Input ontology terms were clustered using the regular Tanimoto index between terms, 𝑇(𝑂1,𝑂2), 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