Functional Analysis of Orofacial Cleft DMRs

To explore the function of any OFC-associated DMRs, we used the missMethyl [35 (link)] R package to test for enrichment of any gene ontology (GO) classification terms or Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. This method corrects for biases in the genomic coverage of the Illumina Infinium HumanMethylation450 BeadChip array. We also looked up gene annotations from our DMRs in recently curated lists of OFC-related genes from (1) the DisGeNET database of diseases and related genes from human, rat and mouse studies [36 (link)] and (2) a bioinformatics study of OFC-related genes in human and animal studies published by Funato et al. [37 (link)].

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Sharp G.C., Ho K., Davies A., Stergiakouli E., Humphries K., McArdle W., Sandy J., Davey Smith G., Lewis S.J, & Relton C.L. (2017). Distinct DNA methylation profiles in subtypes of orofacial cleft. Clinical Epigenetics, 9, 63.

Publication 2017

Infinium HumanMethylation450 BeadChip array

Animal Gene annotations Genes Genomic Human Mouse

Corresponding Organization :

Other organizations : University of Bristol, University Of Bristol Dental Hospital

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Variable analysis

independent variables

Exploration of the function of any OFC-associated DMRs

dependent variables

Enrichment of any gene ontology (GO) classification terms
Enrichment of Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways

control variables

Biases in the genomic coverage of the Illumina Infinium HumanMethylation450 BeadChip array

controls

The missMethyl R package was used to correct for biases in the genomic coverage of the Illumina Infinium HumanMethylation450 BeadChip array.

Annotations

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