Functional enrichment checkpoint: between-group comparison of contrasts (g:Profiler)

Functional enrichment of the genes whose change from monocytes to dendritic cells differs between SLE patients and controls (de_interaction_results), obtained with gprofiler2 in l7_DEGs_between_groups_es.

Usage

go_interaction_results

Format

A data frame with one row per significant term and the same 10 columns as go_results: query, source, term_id, term_name, term_size, query_size, intersection_size, p_value, parents and intersection.

Source

g:Profiler (https://biit.cs.ut.ee/gprofiler/).

Details

Genes with padj < 0.05 were split by the sign of log2FoldChange and queried as four lists (SLEvsCtrl_<UP|DOWN>_<moDC|tolDC>) with gost(organism = "hsapiens", correction_method = "fdr", user_threshold = 0.05, sources = c("GO:BP", "KEGG", "REAC"), evcodes = TRUE).

The archived g:Profiler version e113_eg59_p19 (2025) was used; it is stored in attr(go_interaction_results, "gprofiler_version"). The script that generates it is data-raw/lesson7_checkpoints.R.

See also

de_interaction_results, go_celltype_results

Examples

table(go_interaction_results$query, go_interaction_results$source)
#>                       
#>                        GO:BP KEGG REAC
#>   SLEvsCtrl_DOWN_moDC    228    5   12
#>   SLEvsCtrl_DOWN_tolDC   190    3   14
#>   SLEvsCtrl_UP_moDC      115    0   18
#>   SLEvsCtrl_UP_tolDC      94    2    9