Table 3.
Candidate genes whose methylation is correlated with birth weight
| Data Set | L1-regularized regression R2 1 |
Non-zero regressions/total "leave one out" regressions at maximum L1 R2 | Tissue | Genes in model | Gene ID |
|---|---|---|---|---|---|
| 22 newborns, methylation at 1,536 CpGs assayed using Illumina's GoldenGate array | 0.78 | 21/22 | Blood | APOE | Apolipoprotein E |
| MSX1 | Msh homeobox 1 | ||||
| Placenta | GRB10 | Growth factor receptor-bound protein 10 | |||
| PGRMC1 | Progesterone receptor membrane component 1 | ||||
| RGS14 | Regulator of G-protein signaling 14 | ||||
| SHMT2 | Serine hydroxymethyl transferase 2 (mitochondrial) | ||||
| 48 newborns, methylation at 27,578 CpGs assayed using Illumina's Infinium array | 0.50 | 44/48 | Blood and placenta, as above | Six genes, above | |
| 48 newborns, methylation at 27,578 CpGs assayed using Illumina's Infinium array | 0.70 | 45/48 | Blood | ATP6AP1 | Atpase, H + transporting, lysosomal accessory protein 1 |
| PRSS21 | Protease, serine, 21 (testisin) | ||||
| RCOR1 | REST co-repressor 1 | ||||
| Placenta | ANGPT4 | Angiopoietin 4 | |||
| CDK2 | Cyclin-dependent kinase 2 | ||||
| EVPL | Envoplakin | ||||
| NAT8L | FLJ37478: N-acetyltransferase 8-like (GCN5-related, putative) | ||||
| 48 newborns, methylation at 27,578 CpGs assayed using Illumina's Infinium array | 0.84 | 44/48 | Blood and Placenta, as above | All 13 genes from both experiments, combined |
1 The maximum L1-regularized regression correlation obtained for the gene model in which more than 90% of the "leave one out" cross-validations exhibited non-zero regression parameters (third column)