GO / KEGG Enrichment (gene list)
go_enrichmentTests a gene list for over-representation in GO terms and KEGG pathways using g:Profiler, revealing the biological themes enriched in the set.
Instructions
GO + KEGG over-representation analysis for a gene LIST via g:Profiler g:GOSt (biit.cs.ut.ee/gprofiler; free, no API key). Unlike locus_go_annotations (one locus → its terms), this answers 'what is my gene SET enriched for?' — the dominant question for a differential-expression or co-expression cluster. loci is the query gene list (e.g. AT-codes for Arabidopsis, RAP-DB IDs for rice). sources defaults to GO:BP/GO:MF/GO:CC + KEGG; user_threshold is the g:SCS-corrected significance cutoff (default 0.05). Optional background sets a custom statistical domain (default: all annotated genes). Returns enriched[] (term_id/name/p_value/intersection_size/…, capped at top_n by p-value) plus unmapped[] — query loci g:Profiler could not recognize, surfaced so a locus-namespace mismatch is visible. Defaults to arabidopsis_thaliana; pass organism= for any of the 12 species.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| loci | Yes | Query gene set, e.g. ['AT2G46830', 'AT1G01060', ...] | |
| top_n | No | Max terms returned, sorted by p-value (1–200, default 50) | |
| sources | No | Annotation sources to test (default: all four) | |
| organism | No | Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid | arabidopsis_thaliana |
| background | No | Optional custom statistical background gene set | |
| user_threshold | No | Significance cutoff, g:SCS-corrected (default 0.05) |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mapped | Yes | Loci g:Profiler recognized | |
| sources | Yes | Annotation sources queried | |
| enriched | Yes | ||
| organism | Yes | Canonical organism slug | |
| returned | Yes | Terms in enriched[] after the top_n cap | |
| unmapped | Yes | Loci g:Profiler could not map | |
| query_size | Yes | Number of loci submitted | |
| total_terms | Yes | Significant terms before the top_n cap | |
| gprofiler_id | Yes | g:Profiler organism ID used, e.g. athaliana |