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)

Turan et al. BMC Medical Genomics 2012 5:10   doi:10.1186/1755-8794-5-10

Open Data