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Then select the gene set you want to use (Figure 2). The files available for the current Genome build are listed under the Gene set drop-down list. Click the Finish button to start the analysis.
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By default, the groups are defined by Gene Ontology (GO), a bioinformatics initiative to unify the representation of gene and gene product attributes across various species [1, 2]. There are three main GO groups which are further divided into subgroups:
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The result is stored under an Enrichment task node. To open it, double click on the node or select the respective Task report from the toolbox.
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The contingency table (Figure 5) can be displayed by selecting the View gene breakdown chart icon on the right (
). The term "list" refers to the list of significant genes, while the term "set" refers to the respective GO category. The first row of the contingency table is also seen in the report, namely the Genes in list and Genes not in list columns....
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The View extra details (
) button provides additional information on the GO category (Figure 6). In addition to the details already given in the report, a full list of Genes in list and Genes not in list can be inspected and downloaded (Download data) to the local computer as a text file....
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As previously mentioned, GO identifiers in the first column are hyperlinks to the Gene Ontology web-site entries (an example shown in Figure 7).
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References
- Ashburner M, Ball CA, Blake JA et al. Gene Ontology: tool for the unification of biology. Nat Genetics. 2000; 25:25-29.
- The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015; 43:D1049-1056.Recommended citations from the Geneontology.org website
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