The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration
Abstract
Summary: The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent–child method, as well as topology-based algorithms. A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes/proteins annotated to the term and by linking individual terms to child terms. Availability: The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided: http://compbio.charite.de/ontologizer Requirements: Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool. Contact: sebastian.bauer@charite.de; peter.robinson@charite.de
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Research works printed but not linked: 7
- Alexa, 2006, Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, 22, 1600, 10.1093/bioinformatics/btl140 · DOI · Paper page
- Falcon, 2007, Using GOstats to test gene lists for GO term association, Bioinformatics, 23, 257, 10.1093/bioinformatics/btl567 · DOI · Paper page
- Gansner, 1999, An open graph visualization system and its applications to software engineering, Software Pract. Exper, 30, 1203, 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N · DOI · Paper page
- Grossmann, 2007, Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis, Bioinformatics, 23, 3024, 10.1093/bioinformatics/btm440 · DOI · Paper page
- Khatri, 2005, Ontological analysis of gene expression data: current tools, limitations, and open problems, Bioinformatics, 21, 3587, 10.1093/bioinformatics/bti565 · DOI · Paper page
- Liu, 2003, NetAffx: affymetrix probesets and annotations, Nucleic Acids Res, 31, 82, 10.1093/nar/gkg121 · DOI · Paper page
- Robinson, 2004, Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology, Bioinformatics, 20, 979, 10.1093/bioinformatics/bth040 · DOI
Cited by
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
REVIGO summarizes and visualizes long lists of gene ontology terms
Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021800 · Cited by 6,264
g:Profiler—a web server for functional interpretation of gene lists (2016 update)
Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H., & Vilo, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw199 · Cited by 1,229
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Westermann, A. J., Förstner, K. U., Amman, F., Barquist, L., Chao, Y., Schulte, L. N., Müller, L., Reinhardt, R., Stadler, P. F., & Vogel, J. (2016) · Nature · doi:10.1038/nature16547 · Cited by 499
A high-resolution mRNA expression time course of embryonic development in zebrafish
White, R. J., Collins, J. E., Sealy, I. M., Wali, N., Dooley, C. M., Digby, Z., Stemple, D. L., Murphy, D. N., Billis, K., Hourlier, T., et al. (2017) · eLife · doi:10.7554/elife.30860 · Cited by 361
Metadata
- Authors
- Bauer, S., Grossmann, S., Vingron, M., & Robinson, P. N.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-05-29
- Volume
- 24
- Issue
- 14
- Pages
- 1650-1651
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2116211027
- Cited by
- 495
- References
- 1
- FWCI
- 10.30
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. https://app.cochat.ai/papers/10.1093/bioinformatics/btn250
- The paper
- Bauer, S., Grossmann, S., Vingron, M., & Robinson, P. N. (2008). Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics. https://doi.org/10.1093/bioinformatics/btn250
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
