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Functional enrichment checkpoint: dendritic cells vs monocytes (g:Profiler)

Source: R/go_celltype_results.R
go_celltype_results.Rd

Functional enrichment of the differentially expressed genes (DEG) between dendritic cells and monocytes (de_celltype_results), obtained with gprofiler2 in the lesson about monocyte differentiation (l5_DEGs_monocytes_diff_es).

Usage

go_celltype_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

DEG were defined with |log2FoldChange| >= 1 and padj < 0.05 and queried as eight lists (<Ctrl|SLE>_<UP|DOWN>_<moDC|tolDC>), one at a time, 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_celltype_results, "gprofiler_version"). The script that generates it is data-raw/lesson5_checkpoints.R.

See also

de_celltype_results, go_results

Examples

table(go_celltype_results$query)
#> 
#>  Ctrl_DOWN_moDC Ctrl_DOWN_tolDC    Ctrl_UP_moDC   Ctrl_UP_tolDC   SLE_DOWN_moDC 
#>            1823            2000            1289             974            2077 
#>  SLE_DOWN_tolDC     SLE_UP_moDC    SLE_UP_tolDC 
#>            2155            1016             963