An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Export

@article{citeulike:2925641, abstract = {10.1101/gr.077479.108 We report a novel resource (ethylation rofiles f NA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.}, author = {Rakyan, Vardhman K. and Down, Thomas A. and Thorne, Natalie P. and Flicek, Paul and Kulesha, Eugene and Gr\~{A}¤f, Stefan and Tomazou, Eleni M. and B\~{A}¤ckdahl, Liselotte and Johnson, Nathan and Herberth, Marlis and Howe, Kevin L. and Jackson, David K. and Miretti, Marcos M. and Fiegler, Heike and Marioni, John C. and Birney, Ewan and Hubbard, Tim J. P. and Carter, Nigel P. and Tavar\~{A}{\copyright}, Simon and Beck, Stephan}, citeulike-article-id = {2925641}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.077479.108}, citeulike-linkout-1 = {http://genome.cshlp.org/content/18/9/1518.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/18/9/1518.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18577705}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18577705}, comment = {用MeDIP方法对13种体细胞组织的样本以及胎盘 精子和永生细胞系用新的算法和工具进行了分析，得到第一个解释性的全基因组范围内的组织特异性差分甲基化区域（tDMRs），并且探讨了其意义及同其他表观标记（例如组蛋白修饰）的联系}, day = {24}, doi = {10.1101/gr.077479.108}, issn = {1088-9051}, journal = {Genome Research}, keywords = {2008, bioinformatics, data\_set, dna\_methylation, epigenetics, genome-wide, medip, methylome}, month = {September}, number = {9}, pages = {1518--1529}, posted-at = {2009-11-05 04:19:23}, priority = {2}, title = {An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)}, url = {http://dx.doi.org/10.1101/gr.077479.108}, volume = {18}, year = {2008} }

TY - JOUR ID - citeulike:2925641 L3 - citeulike-article-id:2925641 N2 - 10.1101/gr.077479.108 We report a novel resource (ethylation rofiles f NA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. IS - 9 JF - Genome Research SN - 1088-9051 EP - 1529 TI - An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) VL - 18 SP - 1518 KW - 2008 KW - bioinformatics KW - data_set KW - dna_methylation KW - epigenetics KW - genome-wide KW - medip KW - methylome N1 - 用MeDIP方法对13种体细胞组织的样本以及胎盘 精子和永生细胞系用新的算法和工具进行了分析，得到第一个解释性的全基因组范围内的组织特异性差分甲基化区域（tDMRs），并且探讨了其意义及同其他表观标记（例如组蛋白修饰）的联系 AU - Rakyan, Vardhman AU - Down, Thomas AU - Thorne, Natalie AU - Flicek, Paul AU - Kulesha, Eugene AU - Gräf, Stefan AU - Tomazou, Eleni AU - Bäckdahl, Liselotte AU - Johnson, Nathan AU - Herberth, Marlis AU - Howe, Kevin AU - Jackson, David AU - Miretti, Marcos AU - Fiegler, Heike AU - Marioni, John AU - Birney, Ewan AU - Hubbard, Tim AU - Carter, Nigel AU - Tavaré, Simon AU - Beck, Stephan PY - 2008/09/24/ UR - http://dx.doi.org/10.1101/gr.077479.108 ER -