Analysis: all_ora | Organism: arabidopsis | FDR threshold: 0.05
25 of 25 submitted genes are not among the dataset's measured features; they were added to the background universe: FT, SOC1, FLC, CO, GI, LFY, AP1, FUL, SVP, TFL1.
KEGG ORA completed but returned no enriched pathways. None of the submitted genes may map to KEGG pathways for organism 'ath'.
Reactome analysis could not be completed. The external pathway service may be unreachable — please try again later or contact the administrator.
GO Enrichment
125 significant terms found.
| GO ID | Term | Namespace | Genes | p | FDR |
|---|---|---|---|---|---|
GO:0006355 |
regulation of DNA-templated transcription | biological_process | 16 | 0.00028 | 0.0349 |
GO:0009911 |
positive regulation of flower development | biological_process | 9 | 0.0217 | 0.694 |
GO:0007623 |
circadian rhythm | biological_process | 8 | 0.0357 | 0.694 |
GO:0009908 |
flower development | biological_process | 6 | 0.0909 | 0.694 |
GO:0009909 |
regulation of flower development | biological_process | 6 | 0.0909 | 0.694 |
GO:2000028 |
regulation of photoperiodism, flowering | biological_process | 6 | 0.0909 | 0.694 |
GO:0045893 |
positive regulation of DNA-templated transcription | biological_process | 6 | 0.0909 | 0.694 |
GO:0006357 |
regulation of transcription by RNA polymerase II | biological_process | 5 | 0.141 | 0.694 |
GO:0045944 |
positive regulation of transcription by RNA polymerase II | biological_process | 5 | 0.141 | 0.694 |
GO:0009637 |
response to blue light | biological_process | 5 | 0.141 | 0.694 |
GO:0042752 |
regulation of circadian rhythm | biological_process | 5 | 0.141 | 0.694 |
GO:0010077 |
maintenance of inflorescence meristem identity | biological_process | 4 | 0.215 | 0.694 |
GO:0045892 |
negative regulation of DNA-templated transcription | biological_process | 4 | 0.215 | 0.694 |
GO:0010468 |
regulation of gene expression | biological_process | 4 | 0.215 | 0.694 |
GO:0009409 |
response to cold | biological_process | 4 | 0.215 | 0.694 |
GO:0010228 |
vegetative to reproductive phase transition of meristem | biological_process | 4 | 0.215 | 0.694 |
GO:0010022 |
meristem determinacy | biological_process | 3 | 0.322 | 0.694 |
GO:0009910 |
negative regulation of flower development | biological_process | 3 | 0.322 | 0.694 |
GO:0043153 |
entrainment of circadian clock by photoperiod | biological_process | 3 | 0.322 | 0.694 |
GO:0048510 |
regulation of timing of transition from vegetative to reproductive phase | biological_process | 3 | 0.322 | 0.694 |
GO:0009785 |
blue light signaling pathway | biological_process | 3 | 0.322 | 0.694 |
GO:0009266 |
response to temperature stimulus | biological_process | 2 | 0.476 | 0.694 |
GO:0000160 |
phosphorelay signal transduction system | biological_process | 2 | 0.476 | 0.694 |
GO:0010582 |
floral meristem determinacy | biological_process | 2 | 0.476 | 0.694 |
GO:0010218 |
response to far red light | biological_process | 2 | 0.476 | 0.694 |
GO:0010378 |
temperature compensation of the circadian clock | biological_process | 2 | 0.476 | 0.694 |
GO:0010114 |
response to red light | biological_process | 2 | 0.476 | 0.694 |
GO:0032922 |
circadian regulation of gene expression | biological_process | 2 | 0.476 | 0.694 |
GO:2000024 |
regulation of leaf development | biological_process | 2 | 0.476 | 0.694 |
GO:0010229 |
inflorescence development | biological_process | 2 | 0.476 | 0.694 |
GO:0010321 |
regulation of vegetative phase change | biological_process | 2 | 0.476 | 0.694 |
GO:0006325 |
chromatin organization | biological_process | 2 | 0.476 | 0.694 |
GO:0009408 |
response to heat | biological_process | 2 | 0.476 | 0.694 |
GO:0009416 |
response to light stimulus | biological_process | 2 | 0.476 | 0.694 |
GO:0009638 |
phototropism | biological_process | 2 | 0.476 | 0.694 |
GO:0010244 |
response to low fluence blue light stimulus by blue low-fluence system | biological_process | 2 | 0.476 | 0.694 |
GO:0010617 |
circadian regulation of calcium ion oscillation | biological_process | 2 | 0.476 | 0.694 |
GO:0009739 |
response to gibberellin | biological_process | 2 | 0.476 | 0.694 |
GO:0006511 |
ubiquitin-dependent protein catabolic process | biological_process | 2 | 0.476 | 0.694 |
GO:0016567 |
protein ubiquitination | biological_process | 2 | 0.476 | 0.694 |
GO:0048574 |
long-day photoperiodism, flowering | biological_process | 2 | 0.476 | 0.694 |
GO:0010154 |
fruit development | biological_process | 1 | 0.694 | 0.694 |
GO:0060560 |
developmental growth involved in morphogenesis | biological_process | 1 | 0.694 | 0.694 |
GO:0017148 |
negative regulation of translation | biological_process | 1 | 0.694 | 0.694 |
GO:0006351 |
DNA-templated transcription | biological_process | 1 | 0.694 | 0.694 |
GO:0009736 |
cytokinin-activated signaling pathway | biological_process | 1 | 0.694 | 0.694 |
GO:0010031 |
circumnutation | biological_process | 1 | 0.694 | 0.694 |
GO:0010629 |
negative regulation of gene expression | biological_process | 1 | 0.694 | 0.694 |
GO:0002098 |
tRNA wobble uridine modification | biological_process | 1 | 0.694 | 0.694 |
GO:0002143 |
tRNA wobble position uridine thiolation | biological_process | 1 | 0.694 | 0.694 |
Showing top 50 of 125 — full list in the CSV.
This analysis was not run.
This analysis was not run.
This analysis was not run.
Figures
Enrichment network
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Term–gene membership
Download PNG
Combined terms across databases
| Term | GO p | GO FDR | KEGG p | KEGG FDR | Reactome p | Reactome FDR |
|---|---|---|---|---|---|---|
| regulation of DNA-templated transcription | 0.00028 | 0.0349 | — | — | — | — |
| positive regulation of flower development | 0.0217 | 0.694 | — | — | — | — |
| circadian rhythm | 0.0357 | 0.694 | — | — | — | — |
| flower development | 0.0909 | 0.694 | — | — | — | — |
| regulation of flower development | 0.0909 | 0.694 | — | — | — | — |
| regulation of photoperiodism, flowering | 0.0909 | 0.694 | — | — | — | — |
| positive regulation of DNA-templated transcription | 0.0909 | 0.694 | — | — | — | — |
| regulation of transcription by RNA polymerase II | 0.141 | 0.694 | — | — | — | — |
| positive regulation of transcription by RNA polymerase II | 0.141 | 0.694 | — | — | — | — |
| response to blue light | 0.141 | 0.694 | — | — | — | — |
| regulation of circadian rhythm | 0.141 | 0.694 | — | — | — | — |
| maintenance of inflorescence meristem identity | 0.215 | 0.694 | — | — | — | — |
| negative regulation of DNA-templated transcription | 0.215 | 0.694 | — | — | — | — |
| regulation of gene expression | 0.215 | 0.694 | — | — | — | — |
| response to cold | 0.215 | 0.694 | — | — | — | — |
| vegetative to reproductive phase transition of meristem | 0.215 | 0.694 | — | — | — | — |
| meristem determinacy | 0.322 | 0.694 | — | — | — | — |
| negative regulation of flower development | 0.322 | 0.694 | — | — | — | — |
| entrainment of circadian clock by photoperiod | 0.322 | 0.694 | — | — | — | — |
| regulation of timing of transition from vegetative to reproductive phase | 0.322 | 0.694 | — | — | — | — |
| blue light signaling pathway | 0.322 | 0.694 | — | — | — | — |
| response to temperature stimulus | 0.476 | 0.694 | — | — | — | — |
| phosphorelay signal transduction system | 0.476 | 0.694 | — | — | — | — |
| floral meristem determinacy | 0.476 | 0.694 | — | — | — | — |
| response to far red light | 0.476 | 0.694 | — | — | — | — |
| temperature compensation of the circadian clock | 0.476 | 0.694 | — | — | — | — |
| response to red light | 0.476 | 0.694 | — | — | — | — |
| circadian regulation of gene expression | 0.476 | 0.694 | — | — | — | — |
| regulation of leaf development | 0.476 | 0.694 | — | — | — | — |
| inflorescence development | 0.476 | 0.694 | — | — | — | — |
| regulation of vegetative phase change | 0.476 | 0.694 | — | — | — | — |
| chromatin organization | 0.476 | 0.694 | — | — | — | — |
| response to heat | 0.476 | 0.694 | — | — | — | — |
| response to light stimulus | 0.476 | 0.694 | — | — | — | — |
| phototropism | 0.476 | 0.694 | — | — | — | — |
| response to low fluence blue light stimulus by blue low-fluence system | 0.476 | 0.694 | — | — | — | — |
| circadian regulation of calcium ion oscillation | 0.476 | 0.694 | — | — | — | — |
| response to gibberellin | 0.476 | 0.694 | — | — | — | — |
| ubiquitin-dependent protein catabolic process | 0.476 | 0.694 | — | — | — | — |
| protein ubiquitination | 0.476 | 0.694 | — | — | — | — |
| long-day photoperiodism, flowering | 0.476 | 0.694 | — | — | — | — |
| fruit development | 0.694 | 0.694 | — | — | — | — |
| developmental growth involved in morphogenesis | 0.694 | 0.694 | — | — | — | — |
| negative regulation of translation | 0.694 | 0.694 | — | — | — | — |
| DNA-templated transcription | 0.694 | 0.694 | — | — | — | — |
| cytokinin-activated signaling pathway | 0.694 | 0.694 | — | — | — | — |
| circumnutation | 0.694 | 0.694 | — | — | — | — |
| negative regulation of gene expression | 0.694 | 0.694 | — | — | — | — |
| tRNA wobble uridine modification | 0.694 | 0.694 | — | — | — | — |
| tRNA wobble position uridine thiolation | 0.694 | 0.694 | — | — | — | — |
Method & Provenance
- Method
- Pathway enrichment — GO/KEGG/GSEA
- Method key
pathway(result type:pathway, result #47)- Engine
- Python · scipy/gseapy v1.17.1
- Dataset(s)
- #719 gallery — example_proteomics.csv
- Status
- completed
- Permanent link
- https://cat-g-omxpert.wishartlab.com/pathway/results/by-token/fcbf2775619240969f9aed1551730c97 Bookmark or share this URL — it does not depend on your session.
- Created
- 2026-09-21 02:17:58.014941
Parameters used
| Parameter | Value |
|---|---|
organism | arabidopsis |
namespace | biological_process |
min_gene_count | 1 |
n_input_genes | 25 |
fdr_threshold | 0.05 |
Execution trace
Reconstructed from the parameters stored with this result — represents the Python/R calls the analysis service made.
# GO/KEGG enrichment: hypergeometric test per termfrom scipy.stats import hypergeomp = hypergeom.sf(k - 1, N_background, K_term, n_input)fdr = statsmodels.stats.multitest.multipletests(p_values, method='fdr_bh')# GSEA: gseapy.prerank(rnk=ranked_genes, gene_sets=gmt, seed=seed)Run warnings
- 25 of 25 submitted genes are not among the dataset's measured features; they were added to the background universe: FT, SOC1, FLC, CO, GI, LFY, AP1, FUL, SVP, TFL1.
- KEGG ORA completed but returned no enriched pathways. None of the submitted genes may map to KEGG pathways for organism 'ath'.
- Reactome analysis could not be completed. The external pathway service may be unreachable — please try again later or contact the administrator.