Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes
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{"title"=>"Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes", "type"=>"journal", "authors"=>[{"first_name"=>"I. Hsuan", "last_name"=>"Lin", "scopus_author_id"=>"26633125400"}, {"first_name"=>"Dow Tien", "last_name"=>"Chen", "scopus_author_id"=>"7405455312"}, {"first_name"=>"Yi Feng", "last_name"=>"Chang", "scopus_author_id"=>"55902228800"}, {"first_name"=>"Yu Ling", "last_name"=>"Lee", "scopus_author_id"=>"46961277500"}, {"first_name"=>"Chia Hsin", "last_name"=>"Su", "scopus_author_id"=>"36767750800"}, {"first_name"=>"Ching", "last_name"=>"Cheng", "scopus_author_id"=>"55710450700"}, {"first_name"=>"Yi Chien", "last_name"=>"Tsai", "scopus_author_id"=>"56525874800"}, {"first_name"=>"Swee Chuan", "last_name"=>"Ng", "scopus_author_id"=>"57198815628"}, {"first_name"=>"Hsiao Tan", "last_name"=>"Chen", "scopus_author_id"=>"56525468700"}, {"first_name"=>"Mei Chen", "last_name"=>"Lee", "scopus_author_id"=>"56525503900"}, {"first_name"=>"Hong Wei", "last_name"=>"Chen", "scopus_author_id"=>"57192535354"}, {"first_name"=>"Shih Hui", "last_name"=>"Suen", "scopus_author_id"=>"56526568500"}, {"first_name"=>"Yu Cheng", "last_name"=>"Chen", "scopus_author_id"=>"56526071000"}, {"first_name"=>"Tze Tze", "last_name"=>"Liu", "scopus_author_id"=>"8719753000"}, {"first_name"=>"Chuan Hsiung", "last_name"=>"Chang", "scopus_author_id"=>"57154938800"}, {"first_name"=>"Ming Ta", "last_name"=>"Hsu", "scopus_author_id"=>"7202371205"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"602475479", "sgr"=>"84923346661", "doi"=>"10.1371/journal.pone.0118453", "scopus"=>"2-s2.0-84923346661", "pmid"=>"25706888"}, "id"=>"7eb738b1-71bf-38e8-9f09-4d7f03d3378b", "abstract"=>"Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.", "link"=>"http://www.mendeley.com/research/hierarchical-clustering-breast-cancer-methylomes-revealed-differentially-methylated-expressed-breast", "reader_count"=>50, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>1, "Student > Master"=>9, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1921834"], "description"=>"<p>The genomic regions characterized as enhancer (Enc) or heterochromatin (Htc) in HMEC and MCF7 by ChromHMM were re-annotated as regions that were (A) enhancer in HMEC and MCF7 (B) heterochromatin in HMEC and MCF7, (C) enhancer in HMEC and heterochromatin in MCF7, and (D) enhancer in MCF7 and heterochromatin in HMEC.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316250, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g008", "stats"=>{"downloads"=>0, "page_views"=>45, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_DNA_methylation_levels_of_MCF7_and_HMEC_enhancers_and_or_heterochromatins_in_the_seven_breast_methylomes_/1316250", "title"=>"Distribution of DNA methylation levels of MCF7 and HMEC enhancers and/or heterochromatins in the seven breast methylomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1921846", "https://ndownloader.figshare.com/files/1921847", "https://ndownloader.figshare.com/files/1921848", "https://ndownloader.figshare.com/files/1921849", "https://ndownloader.figshare.com/files/1921850", "https://ndownloader.figshare.com/files/1921851", "https://ndownloader.figshare.com/files/1921852", "https://ndownloader.figshare.com/files/1921853", "https://ndownloader.figshare.com/files/1921854", "https://ndownloader.figshare.com/files/1921855", "https://ndownloader.figshare.com/files/1921856", "https://ndownloader.figshare.com/files/1921858", "https://ndownloader.figshare.com/files/1921859", "https://ndownloader.figshare.com/files/1921860", "https://ndownloader.figshare.com/files/1921861", "https://ndownloader.figshare.com/files/1921862", "https://ndownloader.figshare.com/files/1921863", "https://ndownloader.figshare.com/files/1921864", "https://ndownloader.figshare.com/files/1921865", "https://ndownloader.figshare.com/files/1921866", "https://ndownloader.figshare.com/files/1921867", "https://ndownloader.figshare.com/files/1921868", "https://ndownloader.figshare.com/files/1921869", "https://ndownloader.figshare.com/files/1921870", "https://ndownloader.figshare.com/files/1921871", "https://ndownloader.figshare.com/files/1921872"], "description"=>"<div><p>Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated <i>XIST</i> promoter, reduced expression of <i>XIST</i>, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.</p></div>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316259, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0118453.s001", "https://dx.doi.org/10.1371/journal.pone.0118453.s002", "https://dx.doi.org/10.1371/journal.pone.0118453.s003", "https://dx.doi.org/10.1371/journal.pone.0118453.s004", "https://dx.doi.org/10.1371/journal.pone.0118453.s005", "https://dx.doi.org/10.1371/journal.pone.0118453.s006", "https://dx.doi.org/10.1371/journal.pone.0118453.s007", "https://dx.doi.org/10.1371/journal.pone.0118453.s008", "https://dx.doi.org/10.1371/journal.pone.0118453.s009", "https://dx.doi.org/10.1371/journal.pone.0118453.s010", "https://dx.doi.org/10.1371/journal.pone.0118453.s011", "https://dx.doi.org/10.1371/journal.pone.0118453.s012", "https://dx.doi.org/10.1371/journal.pone.0118453.s013", "https://dx.doi.org/10.1371/journal.pone.0118453.s014", "https://dx.doi.org/10.1371/journal.pone.0118453.s015", "https://dx.doi.org/10.1371/journal.pone.0118453.s016", "https://dx.doi.org/10.1371/journal.pone.0118453.s017", "https://dx.doi.org/10.1371/journal.pone.0118453.s018", "https://dx.doi.org/10.1371/journal.pone.0118453.s019", "https://dx.doi.org/10.1371/journal.pone.0118453.s020", "https://dx.doi.org/10.1371/journal.pone.0118453.s021", "https://dx.doi.org/10.1371/journal.pone.0118453.s022", "https://dx.doi.org/10.1371/journal.pone.0118453.s023", "https://dx.doi.org/10.1371/journal.pone.0118453.s024", "https://dx.doi.org/10.1371/journal.pone.0118453.s025", "https://dx.doi.org/10.1371/journal.pone.0118453.s026"], "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_Clustering_of_Breast_Cancer_Methylomes_Revealed_Differentially_Methylated_and_Expressed_Breast_Cancer_Genes_/1316259", "title"=>"Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921824"], "description"=>"<p>Coloring indicates methylation levels from low (blue) to high (red). Eight distinctive HMR clusters were indicated in each of the three genomic locations. (A) Promoter HMRs. The A-1 cluster represents the promoter HMRs that were consistently lowly methylated in all seven samples. (B) Intragenic HMRs. The B-1, B-2 and B-3 clusters were hypomethylated in one or both cancer cell lines (MCF7 and HCC1954), while other samples remain methylated. (C) Intergenic HMRs. The C-1, C-2 and C-3 clusters were hypomethylated in one or both cancer cell lines (MCF7 and HCC1954), while other samples remain methylated.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316241, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g002", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_of_promoter_intragenic_and_intergenic_HMRs_according_to_their_DNA_methylation_levels_in_the_seven_breast_methylomes_/1316241", "title"=>"Hierarchical clustering of promoter, intragenic and intergenic HMRs according to their DNA methylation levels in the seven breast methylomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921816"], "description"=>"<p>(A) Circos representation of genome-wide DNA methylation levels in the seven breast samples. The data represent the average methylation levels for all of the CpGs in 56,779 50 Kb windows. Coloring indicates methylation levels from low (green) to high (red). (B) The proportion of CpG sites in the DNA that were lowly (< 20%), intermediately (20% ~ 80%) and highly (> 80%) methylated in the seven samples. (C) The proportion of CpG sites in the CGI that were lowly (< 20%), intermediately (20% ~ 80%) and highly (> 80%) methylated in the seven samples. (D) Heatmap representation of average methylation levels of 10 Kb windows with different CpG densities. The CpG density was expressed as the number of CpG sites per 100 bp of nucleotide sequence. Coloring indicates methylation levels from low (green) to high (red). (E) The distribution of the DNA methylation levels of CGI in promoter (TSS ± 1 Kb), intragenic and intergenic regions.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316239, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g001", "stats"=>{"downloads"=>2, "page_views"=>89, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_WGBS_of_a_normal_breast_NB_three_primary_breast_tumors_BT089_BT126_and_BT198_a_mammary_epithelial_cell_line_HMEC_and_two_breast_cancer_cell_lines_MCF7_an_HCC1954_/1316239", "title"=>"WGBS of a normal breast (NB), three primary breast tumors (BT089, BT126 and BT198), a mammary epithelial cell line (HMEC) and two breast cancer cell lines (MCF7 an HCC1954).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921836"], "description"=>"<p>We used chromosome 16 as an examples to illustrate the (A) extent of differential methylation between NB and the other six WGBS datasets, and (B) average predicted PMD size (Kb) along the chromosome. (C) ChIP-chip assay in MCF7 showed PMDs were specifically enriched with H3K27me3 modification. (D) RNA-seq experiments showed genes located within PMDs and extremely large PMDs (> 1 Mb) have very low expression (represented as counts per million, CPM) than those outside PMDs.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316252, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g009", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypomethylation_of_megabase_sized_PMDs_in_breast_tumors_and_cell_lines_/1316252", "title"=>"Hypomethylation of megabase-sized PMDs in breast tumors and cell lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921832"], "description"=>"<p>(A) Proportion of different clusters of HMRs with “low” and “high” regulatory potentials. “Low” potential denotes HMRs that intersect less than four regulatory features, whereas “High” potential HMRs are those that intersect four or more features. A total of eight features were used in the analysis, they are: FANTOM5 TSS, FANTOM5 enhancers, CGI, ENCODE TFBS, ENCODE DNase I hypersensitive sites, MCF7 MNase hypersensitive sites. MCF7 HpaII hypersensitive sites, and RNA PolII binding sites from MCF7 and ENCODE. (B) Proportion of HMRs in each cluster that harbored high levels of ENCODE H3K27me3, H3K4me1, H3K4me2 and H3K27ac. (C) Proportion of HMRs in each cluster that harbored high levels of H3K27me3, H3K4me1, H3K4me3 and CTCF in MCF7. For each histone modification, the HMRs whose score is in the top 20% were considered as having high levels.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316248, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g007", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_of_HMRs_with_cis_elements_and_various_histone_modifications_/1316248", "title"=>"Association of HMRs with <i>cis</i>-elements and various histone modifications.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921830"], "description"=>"<p>(A) Scatter plots of DNA methylation levels of NB (x-axis) and MCF7 and HCC1954 (y-axis; red and blue colors respectively) at promoter regions (TSS ± 1 Kb). The promoter regions that exhibited differential hypomethylation and associated with significant elevated downstream transcript expression (FDR ≤ 0.05) were colored in green. (B) Paired tumor-normal methylation assays of the TCGA BRCA dataset showed two populations of breast cancer patients where one group (colored in red) displayed promoter hypomethylation in the paired tumor samples as compared to the paired normal samples. (C) The group of BRCA patients that showed promoter hypomethylation had significantly reduced expression level of <i>XIST</i> in the corresponding paired tumor samples (t-test, p-value < 0.01). The (D) overall survival and (E) relapse-free survival analysis showed breast cancer patients with lower <i>XIST</i> expression had lower survival probabilities.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316246, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g006", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aberrant_promoter_hypomethylation_of_genes_located_on_the_X_chromosome_in_breast_cancer_cells_/1316246", "title"=>"Aberrant promoter hypomethylation of genes located on the X chromosome in breast cancer cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921827"], "description"=>"<p>The number of HMRs that had sufficient coverage of CpG sites on HumanMethylation450 BeadChip that were used in the plots and the total number of HMRs were provided beside the HMR cluster ID. The effect size for the difference between normal and tumor samples is provided as the d value. General consideration of small, medium and large effect has d values of 0.2, 0.5 and 0.8 respectively. (A) Promoter HMRs. (B) Intragenic HMRs.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316243, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Difference_in_the_distribution_of_DNA_methylation_levels_of_HMRs_between_normal_breast_and_breast_tumor_samples_in_WGBS_and_TCGA_BRCA_datasets_/1316243", "title"=>"Difference in the distribution of DNA methylation levels of HMRs between normal breast and breast tumor samples in WGBS and TCGA BRCA datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1921826"], "description"=>"<p>The differential methylation and differential gene expression between breast cancer cell lines and normal samples were negative correlated in A-3, A-6 and A-8 promoter HMRs. In other HMR clusters, the distributions of differential methylation levels among under-expressed (Under), over-expressed (Over) and not differentially expressed (No DE) genes were similar in form.</p>", "links"=>[], "tags"=>["breast cancer cells", "differentially hypermethylated XIST promoter", "brca", "hmr", "gene expression", "TCGA", "breast tumor samples", "breast tumor methylomes", "dna methylation", "pmd", "breast cancer cell lines", "Breast Cancer Methylomes Revealed Differentially Methylated", "xci", "breast cancer patients", "Breast Cancer Genes Oncogenic transformation", "DNA methylation changes", "DNA methylation data", "breast cancer progression", "mcf"], "article_id"=>1316242, "categories"=>["Biological Sciences"], "users"=>["I-Hsuan Lin", "Dow-Tien Chen", "Yi-Feng Chang", "Yu-Ling Lee", "Chia-Hsin Su", "Ching Cheng", "Yi-Chien Tsai", "Swee-Chuan Ng", "Hsiao-Tan Chen", "Mei-Chen Lee", "Hong-wei Chen", "Shih-Hui Suen", "Yu-Cheng Chen", "Tze-Tze Liu", "Chuan-Hsiung Chang", "Ming-Ta Hsu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118453.g003", "stats"=>{"downloads"=>0, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_differential_methylation_levels_of_gene_promoters_for_under_expressed_over_expressed_and_not_differentially_expressed_genes_between_breast_cancer_cell_lines_MCF7_and_HCC1954_and_normal_breast_samples_NB_and_HMEC_/1316242", "title"=>"Distribution of differential methylation levels of gene promoters for under-expressed, over-expressed and not differentially expressed genes between breast cancer cell lines (MCF7 and HCC1954) and normal breast samples (NB and HMEC).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-23 04:35:37"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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