Table 2. Pathways enriched in DCIS surgical excision specimens (FDR-adjusted P < 0.05).
Genes associated with CpG sites with a Δbeta matched (= beta core biopsy – beta matched surgical) less than 0.15 were analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Top pathways such as no.53, 4514, and 4512 are well known for their roles in wound healing and tissue repair processes. FDR, false discovery rate.
| Pathway ID | Pathway name | Proportion of genes | Raw P-value | FDR-adjusted P-value |
|---|---|---|---|---|
| 53 | Ascorbate and aldarate metabolism | 0.33 | 4.99E-07 | 0.0002 |
| 4940 | Type I diabetes mellitus | 0.23 | 8.29E-06 | 0.0013 |
| 4514 | Cell adhesion molecules (CAMs) | 0.13 | 4.60E-05 | 0.0048 |
| 40 | Pentose and glucuronate interconversions | 0.21 | 2.75E-04 | 0.0095 |
| 860 | Porphyrin and chlorophyll metabolism | 0.19 | 2.44E-04 | 0.0095 |
| 4512 | ECM-receptor interaction | 0.15 | 2.66E-04 | 0.0095 |
| 4724 | Glutamatergic synapse | 0.13 | 2.24E-04 | 0.0095 |
| 5310 | Asthma | 0.23 | 1.37E-04 | 0.0095 |
| 5416 | Viral myocarditis | 0.17 | 1.87E-04 | 0.0095 |
| 983 | Drug metabolism - other enzymes | 0.17 | 4.99E-04 | 0.0155 |
| 4970 | Salivary secretion | 0.13 | 6.67E-04 | 0.0173 |
| 5330 | Allograft rejection | 0.18 | 6.14E-04 | 0.0173 |
| 4080 | Neuroactive ligand-receptor interaction | 0.09 | 7.70E-04 | 0.0184 |
| 4020 | Calcium signaling pathway | 0.10 | 9.45E-04 | 0.0210 |
| 5332 | Graft-versus-host disease | 0.17 | 1.04E-03 | 0.0216 |
| 4713 | Circadian entrainment | 0.12 | 1.23E-03 | 0.0239 |
| 5320 | Autoimmune thyroid disease | 0.15 | 1.44E-03 | 0.0250 |
| 4726 | Serotonergic synapse | 0.12 | 1.90E-03 | 0.0310 |
| 5150 | Staphylococcus aureus infection | 0.14 | 2.15E-03 | 0.0334 |
| 5032 | Morphine addiction | 0.12 | 2.37E-03 | 0.0336 |
| 5200 | Pathways in cancer | 0.08 | 2.37E-03 | 0.0336 |
| 4015 | Rap1 signaling pathway | 0.09 | 2.52E-03 | 0.0340 |
| 140 | Steroid hormone biosynthesis | 0.14 | 2.75E-03 | 0.0343 |
| 4014 | Ras signaling pathway | 0.09 | 2.87E-03 | 0.0343 |
| 4072 | Phospholipase D signaling pathway | 0.19 | 2.79E-03 | 0.0343 |
| 4672 | Intestinal immune network for IgA production | 0.14 | 3.40E-03 | 0.0373 |
| 4730 | Long-term depression | 0.13 | 3.48E-03 | 0.0373 |
| 5033 | Nicotine addiction | 0.15 | 4.09E-03 | 0.0424 |
| 4750 | Inflammatory mediator regulation of TRP channels | 0.11 | 4.75E-03 | 0.0476 |