Table 1.
Gene | Illumina ID | Chr | Mapinfo | WateRmelon | IMA R-package | Gene group | ||
---|---|---|---|---|---|---|---|---|
P value | β diff | P value | β diff | |||||
ABAT Chr16p13 | cg01881182 | 16 | 8806531 | 0.0017 | −0.20 | 0.0047 | −0.15 | 5′ UTR |
cg16586594 | 16 | 8806569 | 0.0005 | −0.18 | 0.0005 | −0.19 | 5′ UTR | |
cg08834902 | 16 | 8806690 | 0.0047 | −0.23 | 0.0047 | −0.16 | 5′ UTR | |
SLC1A6 Chr19p13 | cg12695707 | 19 | 15121333 | 0.0002 | −0.27 | 0.0005 | −0.16 | TSS1500 |
cg09470638 | 19 | 15121509 | 0.0010 | −0.25 | 0.0048 | −0.14 | TSS200 | |
cg02489552 | 19 | 15121531 | 0.0002 | −0.14 | 0.0002 | −0.21 | TSS200 | |
SOX18 Chr20q13 | cg02231404 | 20 | 62679635 | 0.0010 | −0.20 | 0.0010 | −0.21 | Body |
cg22138735 | 20 | 62679713 | 0.0005 | −0.17 | 0.0005 | −0.17 | Body | |
TEPP Chr16q21 | cg04370442 | 16 | 58019866 | 0.0047 | −0.15 | 0.0075 | −0.16 | Body |
cg12499872 | 16 | 58019893 | 0.0005 | −0.31 | 0.0005 | −0.15 | Body | |
CNTNAP1 Chr17q21 | cg16308533 | 17 | 40838983 | 0.0005 | −0.17 | 0.0010 | −0.19 | Body |
cg11629889 | 17 | 40839022 | 0.0002 | −0.14 | 0.0010 | −0.16 | Body | |
SNED1 Chr2q37 | cg23491743 | 2 | 241989271 | 0.0017 | −0.16 | 0.0030 | −0.17 | Body |
cg25241559 | 2 | 241989379 | 0.0005 | −0.15 | 0.0005 | −0.17 | Body |
Selection is performed after analysis with two pipelines and application of three selection criteria: (i) absolute β value difference >0.10; (ii) P value <0.05; and (iii) presence of multiple CpGs per locus. Nucleotide positions accord to NCBI build 37/hg19. Gene group is defined relative to the nearest open reading frame: within 1500 (TSS1500) or 200 bp (TSS200) of a transcription start site, in the 5′ untranslated region (5′ UTR), the first exon of a transcript (exon), in the body of gene (body) or the 3′ UTR (3′ UTR). These six genes were selected for the validation study using Sequenom EpiTYPER
β diff β difference, Chr chromosome, Illumina ID identification according to HM450k, MMC myelomeningocele