We are analyzing https://link.springer.com/protocol/10.1007/978-1-62703-721-1_9.

Title:
Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells | SpringerLink
Description:
DNA methylation, a DNA modification by adding methyl group to cytosine, has an important role in the regulation of gene expression. DNA methylation is known to be associated with gene transcription by interfering with DNA-binding proteins, such as transcription...
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Topics {✒️}

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Schema {🗺️}

ScholarlyArticle:
      headline:Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells
      pageEnd:178
      pageStart:161
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-62703-721-1.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Gene Function Analysis
         isbn:
            978-1-62703-721-1
            978-1-62703-720-4
         type:Book
      publisher:
         name:Humana Press
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Chai-Jin Lee
            affiliation:
                  name:Seoul National University
                  address:
                     name:Seoul National University, Seoul, Korea
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jared Evans
            affiliation:
                  name:Seoul National University
                  address:
                     name:Seoul National University, Seoul, Korea
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Kwangsoo Kim
            affiliation:
                  name:Seoul National University
                  address:
                     name:Seoul National University, Seoul, Korea
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Heejoon Chae
            affiliation:
                  name:Seoul National University
                  address:
                     name:Seoul National University, Seoul, Korea
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Sun Kim
            affiliation:
                  name:Seoul National University
                  address:
                     name:Seoul National University, Seoul, Korea
                     type:PostalAddress
                  type:Organization
            type:Person
      keywords:DNA methylation, Gene expression, Breast cancer, CpG island, CpG shore, Exon, Intron
      description:DNA methylation, a DNA modification by adding methyl group to cytosine, has an important role in the regulation of gene expression. DNA methylation is known to be associated with gene transcription by interfering with DNA-binding proteins, such as transcription factors. DNA methylation is closely related to tumorigenesis, and the methylation state of some genes can be used as a biomarker for tumorigenesis. Aberrant DNA methylation of genomic regions, including CpG islands, CpG shores, and first exons, is related to the altered gene expression pattern characteristics of all human cancers. Subheading 1 surveys recent developments on DNA methylation and gene expressions in cancer. Then we provide analysis of DNA methylation and gene expression in 30 breast cancer cell lines representing different tumor phenotypes. This study conducted an integrated analysis to identify the relationship between DNA methylation in various genomic regions and expression levels of downstream genes, using MethylCapseq data (affinity purification followed by next-generation sequencing of eluted DNA) and Affymetrix gene expression microarray data. The goal of this study was to assess genome-wide methylation profiles associated with different molecular subtypes of human breast cancer (luminal, basal A, and basal B) and to comprehensively investigate the effect of DNA methylation on gene expression in breast cancer phenotypes. This showed that methylation of genomic regions near transcription start sites, CpG island, CpG shore, and first exon was strongly associated with gene repression, and the effects of the regions on gene expression patterns were different for different molecular subtypes of breast cancer. The results further indicated that aberrant methylation of specific genomic regions was significantly associated with different breast cancer subtypes.
      datePublished:2014
      isAccessibleForFree:
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Book:
      name:Gene Function Analysis
      isbn:
         978-1-62703-721-1
         978-1-62703-720-4
Organization:
      name:Humana Press
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:Seoul National University
      address:
         name:Seoul National University, Seoul, Korea
         type:PostalAddress
      name:Seoul National University
      address:
         name:Seoul National University, Seoul, Korea
         type:PostalAddress
      name:Seoul National University
      address:
         name:Seoul National University, Seoul, Korea
         type:PostalAddress
      name:Seoul National University
      address:
         name:Seoul National University, Seoul, Korea
         type:PostalAddress
      name:Seoul National University
      address:
         name:Seoul National University, Seoul, Korea
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Chai-Jin Lee
      affiliation:
            name:Seoul National University
            address:
               name:Seoul National University, Seoul, Korea
               type:PostalAddress
            type:Organization
      name:Jared Evans
      affiliation:
            name:Seoul National University
            address:
               name:Seoul National University, Seoul, Korea
               type:PostalAddress
            type:Organization
      name:Kwangsoo Kim
      affiliation:
            name:Seoul National University
            address:
               name:Seoul National University, Seoul, Korea
               type:PostalAddress
            type:Organization
      name:Heejoon Chae
      affiliation:
            name:Seoul National University
            address:
               name:Seoul National University, Seoul, Korea
               type:PostalAddress
            type:Organization
      name:Sun Kim
      affiliation:
            name:Seoul National University
            address:
               name:Seoul National University, Seoul, Korea
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Seoul National University, Seoul, Korea
      name:Seoul National University, Seoul, Korea
      name:Seoul National University, Seoul, Korea
      name:Seoul National University, Seoul, Korea
      name:Seoul National University, Seoul, Korea
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