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Functional enrichment results checkpoint (g:Profiler)

Source: R/go_results.R
go_results.Rd

Functional enrichment of the differentially expressed genes (DEG) of each cell type, obtained with gprofiler2 in the lesson "Funciones biológicas de los genes diferencialmente expresados" (l4_GOterms_es).

Usage

go_results

Format

A data frame with 943 rows (significant terms) and 10 columns:

query

Gene list (cell type and direction of change).

source

Database: GO:BP, GO:CC, GO:MF, REAC, KEGG, WP, TF, MIRNA, HP or CORUM.

term_id

Term identifier.

term_name

Term name.

term_size

Number of genes annotated to the term.

query_size

Number of genes of the list with annotation in the database.

intersection_size

Number of genes of the list annotated to the term.

p_value

Adjusted p-value (FDR) of the hypergeometric test.

parents

Comma-separated parent terms in the database hierarchy.

intersection

Comma-separated genes of the list annotated to the term.

Source

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

Details

DEG were defined in de_results with |log2FoldChange| >= 1 and padj < 0.05, and queried as five lists (SLE_UP_monocyte, SLE_UP_moDC, SLE_DOWN_moDC, SLE_UP_tolDC, SLE_DOWN_tolDC) with gost(organism = "hsapiens", correction_method = "fdr", user_threshold = 0.05, evcodes = TRUE).

g:Profiler updates its databases periodically. To reproduce the article, the archived version e113_eg59_p19 (June 2025) was used; it is stored in attr(go_results, "gprofiler_version"). The script that generates it is data-raw/lesson4_checkpoints.R.

Examples

table(go_results$query)
#> 
#>   SLE_DOWN_moDC  SLE_DOWN_tolDC     SLE_UP_moDC SLE_UP_monocyte    SLE_UP_tolDC 
#>             291              39               9             322             282 
table(go_results$source)
#> 
#> CORUM GO:BP GO:CC GO:MF    HP  KEGG MIRNA  REAC    TF    WP 
#>    24   556    15    80    65    26     1    47    78    51