Integrative analysis of DNA methylationand gene expression identified breast Cancer-Specific DiagnosticBiomarkers

Introduction: Breast cancer development is accompanied bygenetic and epigenetic alterations that lead to abnormal genefunction. Recent advances in epigenomics knowledge havegreatly impacted our understanding of the mechanisms leadingto breast cancer and, consequently, the development of newstrategies for breast cancer diagnosis and treatment. Epigeneticregulation is known to involve three interacting events: DNAmethylation, histone modifications, and nucleosome remodeling.our study revealed the correlation between DNA methylationand gene expression profiling, which gives modern bitsof knowledge into the part of methylation within the transcriptionalprocess.Method: DNA methylation and gene expression data weredownloaded using TCGAbiolinks from the Cancer Genome Atlas(TCGA) dataset. All cancer tissues and normal tissues werecompared and all high and low methylated genes were lookedfor (FDR<۰.۰۵) using the (TCGAbiolinks) R package. differentially-expressed probes were identified using edgeR. The resulting probes were merged based on delta beta, logFC, andadj.P. Val into five groups namely Hypo methylated -Downregulation,Hypo methylated -Up-regulation, Hyper methylated-Down-regulation, Hyper methylated -Up-regulation, and notsignificant.Result: Based on the result dataset, we found ۱۳۲ significantHyper-Down genes, ۱۶ significant Hyper-Up genes, ۴ significantHypo-Down genes, and ۲ significant Hypo-Up genes.CCL۱۱, SCN۷A, ADAMTS۲۰, and LRRN۳ are importantgenes in Hypo-Up, Hypo-Down, Hyper-Up, and Hyper-Downgroups, respectively.Conclusion: We identified common DNA methylation alterationsin breast cancer at various genomic locations and foundevidence of widespread field effects in breast cancer. Furthermore,we demonstrate the power of combining publicly availablegenomic databases with candidate gene approaches to studycancer epigenetics. We hope to extend our current research onthe role of methylation in breast cancer initiation and developmentby excluding breast cancer-associated methylated genesfrom the TCGA database and analyzing their relationship tobreast cancer progression and prognosis

کلیدواژه ها:

methylation ، breast cancer ، genes expression analysis ، TCGA