goseq output

With these parameters, “goseq” generates three outputs -

  • A table (Ranked category list - Wallenius method) with the following columns for each GO term:

    1. category - GO category

    2. over_rep_pval - p-value for over-representation of the term in differentially expressed genes

    3. under_rep_pval - p-value for under-representation of the term in differentially expressed genes

    4. numDEInCat - number of differentially expressed genes in this category

    5. term - detail of the term

    6. ontology - MF (Molecular Function - molecular activities of gene products), CC (Cellular Component - where gene products are active), BP (Biological Process - pathways and larger processes made up of the activities of multiple gene products)

    7. p.adjust.over_represented - p-value for over-representation of the term in the differentially expressed genes, adjusted for multiple testing with the Benjamini-Hochberg procedure

    8. p.adjust.under_represented - p-value for under-representation of the term in the differentially expressed genes, adjusted for multiple testing with the Benjamini-Hochberg procedure

  • A graph with the top 10 over-represented GO terms

  • A table with the differentially expressed genes associated to the GO terms

Top over represented GO terms

A plot generated by goseq tool showing the top over-represented GO terms