Ontologizer statistics

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Ontologizer specifications

Information


Unique identifier OMICS_10365
Name Ontologizer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.1.2
Stability Stable
Requirements
GraphViz
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Peter Robinson
  • person_outline Sebastian Bauer

Publication for Ontologizer

Ontologizer citations

 (63)
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Translatome Regulation in Neuronal Injury and Axon Regrowth

2018
eNeuro
PMCID: 5944006
PMID: 29756027
DOI: 10.1523/ENEURO.0276-17.2018
call_split See protocol

[…] e “cosine” option was used for distance measurement (“Pdist value”) using average linkage (“LinkageValue”). No standardization was used. Gene ontology (GO) term enrichment analyses were done with the Ontologizer GO analysis tool (; http://ontologizer.de/webstart/), using total genome entries as background and the topology-weighted algorithm to identify-enriched GO terms. […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] d death model for the statistical analysis of the evolution of gene family size, was applied to identify gene families that had undergone expansion and/or contraction. The GO enrichment was done with Ontologizer 2.0 by using one-sided Fisher’s exact test, the Parent-Child-Union method, with a p-value cut-off of 0.01. All genes with GO annotation were used as reference, and the genes undergone expa […]

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MFS Transporters and GABA Metabolism Are Involved in the Self Defense Against DON in Fusarium graminearum

2018
Front Plant Sci
PMCID: 5908970
PMID: 29706976
DOI: 10.3389/fpls.2018.00438
call_split See protocol

[…] s described previously (). GO annotation was carried out with Blast2GO (), and GO enrichment analysis was performed by the parent–child union method with Benjamini–Hochberg correction as developed in Ontologizer (). […]

library_books

Detection of Plant miRNAs Abundance in Human Breast Milk

2017
Int J Mol Sci
PMCID: 5795987
PMID: 29295476
DOI: 10.3390/ijms19010037

[…] /www.genome.jp/tools/kaas/) [] was used, which performed Blastn comparison against the manually validated set of human genes in the KEGG GENES database. The GO enrichment was done with the use of the Ontologizer program [] and the predicted miRNA targets served as a study set. In turn, all the available human sequences collected from the Ensemble Gene database served as the population set. The “Te […]

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BMPs as new insulin sensitizers: enhanced glucose uptake in mature 3T3 L1 adipocytes via PPARγ and GLUT4 upregulation

2017
Sci Rep
PMCID: 5722815
PMID: 29222456
DOI: 10.1038/s41598-017-17595-5
call_split See protocol

[…] and a standard deviation of one. Based on these vectors hierarchical clustering was performed and five clusters were identified by visual inspection. MGSA and Parent-Child-Intersection method of the Ontologizer were used for GO analyses. GO terms with Bonferroni corrected p < 0.05 were considered as significant. PPARγ target genes were derived from Nackachi et al.. […]

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The Gene Ontology of eukaryotic cilia and flagella

2017
Cilia
PMCID: 5688719
PMID: 29177046
DOI: 10.1186/s13630-017-0054-8
call_split See protocol

[…] [] was obtained from CilDB [] and the resulting list of Ensembl protein identifiers were converted to gene symbols in Ensembl biomart (version 86) []. Term enrichment analysis was performed using the Ontologizer 2.1 [] using the Parent–Child–Union method and applying the Bonferroni multiple testing correction. A custom R script was used to generate graphs to compare two term enrichment analyses fo […]

Citations

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Ontologizer institution(s)
Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Max-Planck-Institute for Molecular Genetics, Berlin, Germany
Ontologizer funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (SFB 760).

Ontologizer review

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Anonymous user #5339

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Desktop
Very versatile tool. Especially for poor-annotated species, as required gene.association file could be constructed and provided to software by user. With more work it is possible to use this tool for term enrichment in other classifications, eg. InterPro. The webstart version not always work in linux, but command-line version (not hard to handle) does. The software draw also nice graphs, using GraphViz. Among statistical options are several computation methods, several multiple comparison correction procedures, and accounting for hierarchical structure of GO classification.