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GOEnrichment (version 2.0.1)
Gene Ontology file in OBO or OWL format (see http://geneontology.org/docs/download-ontology
Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)
File containing the gene products corresponding to the study set (one per line)
File containing the gene products corresponding to the population set (one per line). If no file is submitted, the population set will be the set of all gene products listed in the annotation file.
The multiple test correction method to use (Benjamini-Hochberg is recommended).
The corrected p-value (or q-value) cut-off to apply for the graph output.
The format of the output graphs (png, svg, or tabular for importing into cytoscape).
Whether to produce a summarized list of GO terms or the full list of those that are statistically significant
Whether to exclude GO terms that are annotated to a single gene product in the study set
Whether to infer annotations through 'part_of' and other non-hierarchical relationships, or only through 'is_a' relations

GOEnrichment is a Java application that can be used to analyze gene product sets (e.g., from microarray or RNAseq experiments) for enriched GO terms.


GOEnrichment requires:


GOEnrichment produces a tabular result file and a graph file for each GO type (MF - Molecular Function, BP - Biological Process and CC - Cellular Component):


The graph is colored by p-value: terms with p-value above cut-off appear in white; and the color gets darker as the p-value decreases

https://github.com/DanFaria/GOEnrichment/raw/master/Scale.png

(see the scale at https://github.com/DanFaria/GOEnrichment/blob/master/Scale.png). In addition to the name of each GO term, the graph shows its frequency in the study set. Dashed edges indicate that one or more intermediate terms were ommited from the graph.


Gene products listed in either the study or population set files that are not present in the annotation file will be ignored.