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Table 1 Top six differentially methylated genes investigated by HM450k and selected for validation with Sequenom EpiTYPER

From: Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development

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
  1. 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
  2. β diff β difference, Chr chromosome, Illumina ID identification according to HM450k, MMC myelomeningocele