Table 1.
Selected overrepresented gene sets associated with each H3K4me3 pattern
| 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 |
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