Table 7

Five random permutation models with higher R2 than the L1 model and the adjusted R2 when tested on the Infinium data-set

Data Set

R2

Adjusted R2 and stability when tested on Infinium Data

Genes in model

Gene names


22 newborns, methylation at 1,536 CpGs assayed using Illumina's GoldenGate array

0.86

0.59 (46/48)

ADAM9

ADAM metallopeptidase domain 9

DPYSL3

dihydropyrimidinase-like 3

FABP5

fatty acid binding protein 5

HOXB4

homeobox B4

MHC2TA

CIITA, class II, major histocompatibility complex, transactivator

PRO1853

C2orf56, chromosome 2 open reading frame 56

0.82

negative

GRB10

growth factor receptor-bound protein 10

HRASLS3

PLA2G16, phospholipase A2, group XVI

MYH14

myosin, heavy chain 14, non-muscle

NM15555

WNT16

wingless-type MMTV integration site family, member 16

0.81

0.48 (44/48)

BEST1

bestrophin 1

IMPDH2

IMP (inosine 5'-monophosphate) dehydrogenase 2

OSBPL5

oxysterol binding protein-like 5

PAX3

paired box 3

PSMC3

proteasome (prosome, macropain) 26S subunit, ATPase, 3

SERPINF1

serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1

0.80

0 (45/48)

CBX1

chromobox homolog 1

EOMES

eomesodermin

PABPC4

poly(A) binding protein, cytoplasmic 4 (inducible form)

PIK3CG

phosphoinositide-3-kinase, catalytic, gamma polypeptide

SLC16A1

solute carrier family 16, member 1 (monocarboxylic acid transporter 1)

TMPO

thymopoietin

0.79

negative

C11ORF15

TMEM9B, TMEM9 domain family, member B

CCT3

chaperonin containing TCP1, subunit 3 (gamma)

MYH9

myosin, heavy chain 9, non-muscle

PROX1

prospero homeobox 1

REST

RE1-silencing transcription factor

RPS2

ribosomal protein S2


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

Open Data