Analysis of methylation microarray for tissue specific detection

dc.contributor.authorTachapol Muangsuben_US
dc.contributor.authorJarunya Samsuwanen_US
dc.contributor.authorPumipat Tongyooen_US
dc.contributor.authorNakarin Kitkumthornen_US
dc.contributor.authorApiwat Mutiranguraen_US
dc.contributor.otherChulalongkorn Universityen_US
dc.contributor.otherPolice General Hospitalen_US
dc.contributor.otherMahidol Universityen_US
dc.description.abstract© 2014 Elsevier B.V. The role of human DNA methylation has been extensively studied in genomic imprinting, X-inactivation, and disease. However, studies of tissue-specific methylation remain limited. In this study, we use bioinformatics methods to analyze methylation data and reveal loci that are exclusively methylated or unmethylated in individual tissues. We collect 39 previously published DNA methylation profiles using an Illumina® HumanMethylation 27 BeadChip Kit containing 22 common tissues and involving 27,578 CpG loci across the human genome. We found 86 positions of tissue specific methylation CpG (TSM) that encompass 34 hypermethylated TSMs (31 genes) and 52 hypomethylated TSMs (47 genes). Tissues were found to contain 1 to 25 TSM loci, with the majority in the liver (25), testis (18), and brain (16). Fewer TSM loci were found in the muscle (8), ovary (7), adrenal gland (3), pancreas (2-4), kidney, spleen, and stomach (1 each). TSMs are predominantly located 0-300 base pairs in the 3' direction after the transcription start site. Similar to known promoters of methylation, hypermethylated TSM genes suppress transcription, while hypomethylated TSMs allow gene transcription. The majority of hypermethylated TSM genes encode membrane proteins and receptors, while hypomethylated TSM genes primarily encode signal peptides and tissue-specific proteins. In summary, the database of TSM loci produced herein is useful for the selection of tissue-specific DNA markers as diagnostic tools, as well as for the further study of the mechanisms and roles of TSM.en_US
dc.identifier.citationGene. Vol.553, No.1 (2014), 31-41en_US
dc.rightsMahidol Universityen_US
dc.subjectBiochemistry, Genetics and Molecular Biologyen_US
dc.titleAnalysis of methylation microarray for tissue specific detectionen_US