2009
Genome-wide screen of promoter methylation identifies novel markers in melanoma
Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Research 2009, 19: 1462-1470. PMID: 19491193, PMCID: PMC2720187, DOI: 10.1101/gr.091447.109.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultAgedBiomarkers, TumorCells, CulturedCluster AnalysisCollagenCollagen Type IDNA MethylationFemaleGene Expression ProfilingGenome-Wide Association StudyGenome, HumanHSP20 Heat-Shock ProteinsHumansInfant, NewbornMaleMelanomaMetallothioneinMiddle AgedMolecular ChaperonesNuclear ProteinsNucleoplasminsOligonucleotide Array Sequence AnalysisPhosphoproteinsPromoter Regions, GeneticProteinsReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionSequence Analysis, DNATumor Cells, CulturedConceptsDifferential gene expressionGene expressionPromoter methylationGenome-wide promoter methylationGenome-wide integrative analysisPromoter CpG contentMethylation markersGenome-wide screenSequencing of bisulfiteTranscription start siteMelanoma cell strainsCell strainsTranscriptional machineryNovel genesEpigenetic modificationsDNA methylationIdentifies novel markersStart siteSnap-frozen tissuesCpG contentAdult melanocytesIntegrative analysisReal-time reverse transcriptase PCRHuman diseasesMethylation
2008
MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Research 2008, 18: 1652-1659. PMID: 18765822, PMCID: PMC2556264, DOI: 10.1101/gr.080721.108.Peer-Reviewed Original ResearchConceptsDNA methylation levelsDNA methylationMethylation levelsRelative DNA methylation levelsChromosome-wide levelBisulfite genomic DNA sequencingGenome-wide studiesMelanoma cell strainsDNA methylation statusGenomic DNA sequencingTranscriptional machineryNormal human melanocytesMethylated CpGsMethylated fragmentsEpigenetic modificationsMethylation estimatesHigh-throughput settingHuman diseasesHuman melanocytesMethylationMethylation statusDNA sequencingAntibody enrichmentGenomeCell strains