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Peer-reviewedCC BY 4.0NAR Genomics and Bioinformatics

Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis

  • Lukas Ramlow1
  • Jasmin Scholtes1
  • Daniel Danis1
  • Peter N Robinson1,2
  1. 1Berlin Institute of Health at Charité Universitätsmedizin , Luisenstr. 65, 10117, Berlin ,
  2. 2The Jackson Laboratory for Genomic Medicine , 10 Discovery Drive, 06032, Connecticut ,
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Abstract

We present Ontologizer 3, an easy-to-use cross-platform desktop application for Gene Ontology (GO) overrepresentation analysis. Ontologizer 3 offers two complementary methods. The first is a frequentist approach that evaluates GO terms individually using a one-sided Fisher’s exact test, yielding term-level significance values. The second is a Bayesian approach that jointly evaluates terms using model-based gene set analysis (MGSA), yielding term-level posterior probabilities. Due to substantial overlap among annotated gene sets resulting from the GO’s hierarchical structure, the two methods produce different results. The frequentist approach tends to report a lengthy list of terms with strong annotation overlap, whereas, MGSA yields a parsimonious set of terms that explain the observed gene activity. Using simulated data with a known ground truth, we demonstrate that both methods reliably identify the causal term, but MGSA achieves substantially higher precision. Ontologizer 3 is implemented as a Tauri application with a Rust backend and an Angular frontend, presenting enriched terms in tabular and graphical form. The software is freely available under the MIT licence at https://github.com/P2GX/ontologizer-gui. Installation packages for Macintosh, Windows, and Debian-based Linux are available on the GitHub Releases page.

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Cite

BibTeXRIS
BibTeX
@article{ramlow2026ontologizer,
  title = {{Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis}},
  author = {Lukas Ramlow and Jasmin Scholtes and Daniel Danis and Peter N Robinson},
  journal = {NAR Genomics and Bioinformatics},
  year = {2026},
  month = nov,
  doi = {10.1093/nargab/lqag131},
  url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag131/9010724},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis
AU  - Lukas Ramlow
AU  - Jasmin Scholtes
AU  - Daniel Danis
AU  - Peter N Robinson
PY  - 2026
DA  - 2026/11/03
JO  - NAR Genomics and Bioinformatics
DO  - 10.1093/nargab/lqag131
UR  - https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag131/9010724
AB  - We present Ontologizer 3, an easy-to-use cross-platform desktop application for Gene Ontology (GO) overrepresentation analysis. Ontologizer 3 offers two complementary methods. The first is a frequentist approach that evaluates GO terms individually using a one-sided Fisher’s exact test, yielding term-level significance values. The second is a Bayesian approach that jointly evaluates terms using model-based gene set analysis (MGSA), yielding term-level posterior probabilities. Due to substantial overlap among annotated gene sets resulting from the GO’s hierarchical structure, the two methods produce different results. The frequentist approach tends to report a lengthy list of terms with strong annotation overlap, whereas, MGSA yields a parsimonious set of terms that explain the observed gene activity. Using simulated data with a known ground truth, we demonstrate that both methods reliably identify the causal term, but MGSA achieves substantially higher precision. Ontologizer 3 is implemented as a Tauri application with a Rust backend and an Angular frontend, presenting enriched terms in tabular and graphical form. The software is freely available under the MIT licence at https://github.com/P2GX/ontologizer-gui. Installation packages for Macintosh, Windows, and Debian-based Linux are available on the GitHub Releases page.
SN  - 2631-9268
ER  -