GOTrapper. A tool to navigate through branches of gene ontology hierarchy

Hassan H, Shanak S (2019)
BMC Bioinformatics 20(1): 20.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up with different hypotheses and help further investigations of an experiment. The biological function for desired genes and gene associations is picked up from a randomly chosen list or through the analysis of differential gene expression. Many tools have been developed to utilize GO knowledge and cluster genes according to relevant biological functions. The retrieved GO terms include both specific and non-specific terms, which is not user-friendly in terms of data analysis. Thus one approach is still missing, which allows navigating through different levels of GO hierarchy manually. Result We developed a tool, GOTrapper, which allows moving up or down to the very bottom of the GO hierarchy. This is performed manually by the user, based on an assigned threshold. This tool grabs the shared terms by the desired set of input genes of Homo sapiens. Here, two inputs are possible. “Within” is to find associated terms within one gene list, and “Between” is to find associated terms between two lists. The tool also provides the option to return the terms with the pre-selected evidence codes. Conclusion GOTrapper is a user-friendly Java tool that helps the user move up and down the ontology tree, which leads to new hypotheses and devising new association of the input genes. It also allows returning terms of associated genes based on selected evidence codes. This tool can be accessed and is freely available at https://github.com/BioGeneTools/GOTrapper.
Stichworte
Gene ontology GO term refinement Gene association
Erscheinungsjahr
2019
Zeitschriftentitel
BMC Bioinformatics
Band
20
Ausgabe
1
Art.-Nr.
20
eISSN
1471-2105
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
Page URI
https://pub.uni-bielefeld.de/record/2933161

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Hassan H, Shanak S. GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics. 2019;20(1): 20.
Hassan, H., & Shanak, S. (2019). GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics, 20(1), 20. doi:10.1186/s12859-018-2581-8
Hassan, H., and Shanak, S. (2019). GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics 20:20.
Hassan, H., & Shanak, S., 2019. GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics, 20(1): 20.
H. Hassan and S. Shanak, “GOTrapper. A tool to navigate through branches of gene ontology hierarchy”, BMC Bioinformatics, vol. 20, 2019, : 20.
Hassan, H., Shanak, S.: GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics. 20, : 20 (2019).
Hassan, Hezha, and Shanak, Siba. “GOTrapper. A tool to navigate through branches of gene ontology hierarchy”. BMC Bioinformatics 20.1 (2019): 20.
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2019-09-06T09:19:05Z
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