Pathway Result #47 — Analysis Report

Generated 2026-09-21 02:38:59 · 1 run · CAT-G Data Analyzer

Contents

pathway (#47) completed

1. Pathway 2026-09-21 02:17:58 · pathway

Enrichment analysis found 125 significant term(s) across the queried databases.

go

go_id	go_term	namespace	gene_count	bg_count	gene_ratio	bg_ratio	p_value	fdr	genes
GO:0006355	regulation of DNA-templated transcription	biological_process	16	16	0.64	0.444444	0.00028	0.034945	['AGL24', 'AP1', 'CDF1', 'COL1', 'FD', 'FKF1', 'FUL', 'FWA', 'GI', 'LFY', 'LHY', 'PHYB', 'SOC1', 'SPL3', 'SVP', 'TOC1']
GO:0009911	positive regulation of flower development	biological_process	9	9	0.36	0.25	0.021701	0.694444	['CRY2', 'FD', 'FKF1', 'FT', 'FUL', 'FWA', 'SOC1', 'SPL3', 'TSF']
GO:0007623	circadian rhythm	biological_process	8	8	0.32	0.222222	0.035742	0.694444	['CCA1', 'COL1', 'CRY2', 'FKF1', 'GI', 'LHY', 'TOC1', 'ZTL']
GO:0009908	flower development	biological_process	6	6	0.24	0.166667	0.090923	0.694444	['AP1', 'GI', 'LFY', 'SOC1', 'SPL3', 'ZTL']
GO:0009909	regulation of flower development	biological_process	6	6	0.24	0.166667	0.090923	0.694444	['COL1', 'CRY2', 'FD', 'FT', 'FWA', 'LFY']
GO:2000028	regulation of photoperiodism, flowering	biological_process	6	6	0.24	0.166667	0.090923	0.694444	['COL1', 'CRY2', 'FD', 'GI', 'LHY', 'PHYB']
GO:0045893	positive regulation of DNA-templated transcription	biological_process	6	6	0.24	0.166667	0.090923	0.694444	['AGL24', 'AP1', 'CCA1', 'FD', 'SOC1', 'SPL3']
GO:0006357	regulation of transcription by RNA polymerase II	biological_process	5	5	0.2	0.138889	0.140931	0.694444	['AGL24', 'AP1', 'FUL', 'SOC1', 'SVP']
GO:0045944	positive regulation of transcription by RNA polymerase II	biological_process	5	5	0.2	0.138889	0.140931	0.694444	['AGL24', 'AP1', 'FUL', 'SOC1', 'SVP']
GO:0009637	response to blue light	biological_process	5	5	0.2	0.138889	0.140931	0.694444	['CRY2', 'FKF1', 'GI', 'LHY', 'ZTL']

enrichment network

term gene heatmap

Method & Provenance

Method: Pathway enrichment — GO/KEGG/GSEA
Engine: Python · scipy/gseapy 1.17.1
Input dataset: gallery — example_proteomics.csv
Started: 2026-09-21 02:17:58.014941
Permanent link: https://cat-g-omxpert.wishartlab.com/pathway/results/by-token/fcbf2775619240969f9aed1551730c97

Parameter	Value
organism	arabidopsis
namespace	biological_process
min_gene_count	1
n_input_genes	25
fdr_threshold	0.05

Command history

# python
# GO/KEGG enrichment: hypergeometric test per term
# python
from scipy.stats import hypergeom
# python
p = hypergeom.sf(k - 1, N_background, K_term, n_input)
# python
fdr = statsmodels.stats.multitest.multipletests(p_values, method='fdr_bh')
# python
# GSEA: gseapy.prerank(rnk=ranked_genes, gene_sets=gmt, seed=seed)