Performs GO term enrichment using TopGO2 R package
A class that wraps the TopGO2 R package for performing GO enrichment analysis on gene list data.
TopGO2 is an open-source R pakage for performing GO enrichment analysis using the Gene Ontology (GO) database.
Alexa A, Rahnenfuhrer J (2022). topGO: Enrichment Analysis for Gene Ontology. R package version 2.50.0.
More information here: https://bioconductor.org/packages/release/bioc/html/topGO.html
[Mandatory]: - Gene list file must contains genes, one per line.
- The gene univers file is a tab-delimited text file format where each row contains as a first column gene ID followed by (
) a list of associated GO term separeted by "," (GO:XXXXXX)
Here's are examples of a Gene Universe File and Gene List File for performing GO term enrichment analysis:
- Gene list files : Gene_0102 Gene_0708 ... Gene_0909 - Gene universe file (tab separated) : # Gene ontology enrichment analysis Gene_0001 GO:0008150, GO:0009987, GO:0016192, GO:0050896 Gene_0002 Gene_0003 GO:0050896 ... Gene_2305 GO:001234 OR .gmt GSEA db files (see documentation here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29 ) : # Gene ontology enrichment analysis GO:0000001 NA Gene_00012 Gene_00018 Gene_00019 Gene_00011 GO:0000002 Here is a description of the gene Gene_00735 Gene_01257 GO:0000003 NA Gene_00012 ... GO:0050896 NA Gene_00018 Gene_00019
Gene Universe File format (see Documentation above)
Top X results Fisher's Text p-value based (see TOPGO documentation)