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Table 1 Selected overrepresented gene sets associated with each H3K4me3 pattern

From: H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus

H3K4me3 Source Name N Odds ratio p value FDR
Narrow peak BioSystems tRNA metabolic process 28 4.001 1.68E–18 1.29E–14
Narrow peak BioSystems Oxidative phosphorylation 11 4.494 1.68E–09 4.39E–07
Narrow peak KEGG Exon junction complex (EJC) 4 7.094 8.03E–06 4.46E–04
Narrow peak BioSystems RNA polymerase II core binding 4 6.305 1.66E–05 7.59E–04
Upstream extended MSigDb FOXM1 38 2.304 2.39E–10 3.68E–06
Upstream extended MSigDb PAX4 42 2.003 7.99E–09 3.73E–05
Upstream extended MSigDb MYOD 31 2.225 2.09E–08 5.36E–05
Upstream extended KEGG Systemic lupus erythematosus 22 1.572 1.07E–03 5.61E–02
Downstream extended KEGG Hematopoietic cell lineage 27 14.792 1.24E–30 1.85E–28
Downstream extended KEGG Staphylococcus aureus infection 13 9.427 1.98E–13 3.90E–12
Downstream extended MSigDb Systemic lupus erythematosus 12 5.216 2.53E–09 2.50E–08
Downstream extended BioSystems Response to interferon-alpha 8 8.681 1.23E–08 1.09E–07
Broad symmetric BioSystems RORA activates gene expression 11 14.111 1.02E–15 3.65E–14
Broad symmetric BioSystems DNA binding, bending 8 12.285 2.28E–11 3.97E–10
Broad symmetric MSigDb HMX1 10 6.987 9.52E–11 1.48E–09
Broad symmetric KEGG Systemic lupus erythematosus 18 2.198 4.11E–06 2.44E–05
  1. Source: The original database that defines the gene set, Name original gene set name, N number of genes belong to both the H3K4me3 pattern and the gene set, Odds ratio relative enrichment, p value hypergeometric test p value, FDR false discovery rate by Benjamini/Hochberg method