Documentation PlantQTLdb Assistant Functional Enrichment with g:Profiler
Browse Documentation
Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Functional Enrichment with g:Profiler

find over-represented functions in a gene set and understand adjusted P values and experimental backgrounds

Requires Research mode

Open PlantQTLdb Assistant

When to use it

Analyze a set of candidate genes or differentially expressed genes. Provide 2–500 identifiers from one species. For an experiment, use all tested genes as the background rather than only significant genes.

How to ask and what you receive

Try a small demonstration set

ask
Run g:Profiler functional enrichment for Arabidopsis genes AT1G01010 AT1G01020 AT1G01030 AT1G01040

what you receive

A term table with FDR-adjusted P values, hit sizes and mapped genes; a chart of up to the first ten returned terms; JSON, CSV and SVG downloads. This demonstration returned 63 terms during verification, not a promised count for future data releases.

Specify the tested-gene background

ask
Run g:Profiler functional enrichment with these parameters
```json
{"species":"arabidopsis","genes":["AT1G01010","AT1G01020"],"background":["AT1G01010","AT1G01020","AT1G01030","AT1G01040"],"sources":["GO:BP","GO:MF","GO:CC"]}
```

what you receive

An analysis using the supplied background. This small example illustrates input format and may have no significant terms. Replace both lists with your actual experiment; every query gene must be included in the background.

Actual g:Profiler result card with adjusted P values and a ten-term bar chart
Production verification, 12 September 2026. The chart is a preview; returned terms are available in the download.

Read the statistics

Enrichment is not causal evidence. No significant term is a valid possible result; it does not prove that the genes lack a shared function.

Adjusted P value
The returned value is already corrected by FDR. Do not treat it as an unadjusted P value.
Bar length
−log10(FDR-adjusted P value). A longer bar indicates stronger statistical support, not a larger biological effect.
Mapped and unmapped genes
Mapping determines which inputs enter the analysis. Check failed or ambiguous identifiers before interpreting the output.

Coverage and limits

  • GO categories are the default; pathway sources depend on provider and species coverage. At most 100 terms are returned, with truncation marked.
  • Gossypium hirsutum and Gossypium arboreum are currently unsupported. The tool explains why it did not run and does not substitute a different cotton species.
  • Up to 20,000 background identifiers are supported, subject also to the message length limit. Without an explicit background, the provider's annotated-gene background is used and reported.