Table 3. Co-methylation modules defined in CANDLE newborn cord blood.
| Gene Ontology (GO) enrichment 1 | ||||||||
|---|---|---|---|---|---|---|---|---|
| Module | Size | Top GO | p-value | FDR | Ancestry 2 | Vit D 2 | Lymph 2 | Gran2 |
| Meth1 3 | 7924 | GO:0010605~negative regulation of macromolecule metabolic process | 3.1E-11 | 1.6E-07 | 0.03 | |||
| GO:0042981~regulation of apoptosis | 3.3E-11 | 8.4E-08 | ||||||
| Meth2 | 2430 | GO:0006952~defense response | 6.5E-14 | 2.6E-10 | ||||
| Meth3 | 2231 | GO:0030182~neuron differentiation | 4.4E-11 | 1.8E-07 | ||||
| Meth4 | 2104 | GO:0006952~defense response | 3.9E-08 | 1.35E-04 | 0.02 | 0.007 | ||
| Meth5 | 1917 | GO:0006955~immune response | 1.4E-18 | 5.5E-15 | 4.3E-05 | 1.8E-61 | 9.8E-50 | |
| Meth6 | 1895 | GO:0010522~regulation of calcium ion transport into cytosol | 2.0E-05 | 0.07 | 0.02 | 0.02 | 0.007 | |
| Meth7 | 641 | GO:0010033~response to organic substance | 2.8E-05 | 0.07 | 0.0004 | 0.006 | ||
| Meth8 | 584 | GO:0043067~regulation of programmed cell death | 6.4E-07 | 0.002 | ||||
| Meth9 | 160 | GO:0051252~regulation of RNA metabolic process | 0.002 | 0.8 | 0.03 | |||
1Top Biological Process GO term; enrichment p-value based on modified Fisher’s exact test from DAVID and Benjamini FDR corrected p-value (http://david.abcc.ncifcrf.gov).
2Association between module eigengenes and ancestry, maternal vitamin D, and estimated fraction of lymphocytes (Lymph) and granulocytes (Gran) based on simple regression analysis; these are uncorrected p-values.
3Meth1 is the largest module and the GO analysis was done for the top 5,000. Top 2 GO categories shown.