Cedar H, Bergman Y: Programming of DNA methylation patterns. Annu Rev Biochem. 2012, 81: 97-117. 10.1146/annurev-biochem-052610-091920.
Article
CAS
PubMed
Google Scholar
Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, Yang AS: Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue-and individual-specific DNA methylation patterns. Hum Mol Genet. 2009, 18: 4808-4817. 10.1093/hmg/ddp445.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, Tomazou EM, Backdahl L, Johnson N, Herberth M, et al: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 2008, 18: 1518-1529. 10.1101/gr.077479.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J, et al: A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008, 6: e22-10.1371/journal.pbio.0060022.
Article
PubMed Central
PubMed
Google Scholar
Song F, Mahmood S, Ghosh S, Liang P, Smiraglia DJ, Nagase H, Held WA: Tissue specific differentially methylated regions (TDMR): changes in DNA methylation during development. Genomics. 2009, 93: 130-139. 10.1016/j.ygeno.2008.09.003.
Article
PubMed Central
CAS
PubMed
Google Scholar
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Sung KWK, Rigoutsos I, Loring J: Dynamic changes in the human methylome during differentiation. Genome Res. 2010, 20: 320-331. 10.1101/gr.101907.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nagae G, Isagawa T, Shiraki N, Fujita T, Yamamoto S, Tsutsumi S, Nonaka A, Yoshiba S, Matsusaka K, Midorikawa Y: Tissue-specific demethylation in CpG-poor promoters during cellular differentiation. Hum Mol Genet. 2011, 20: 2710-2721. 10.1093/hmg/ddr170.
Article
CAS
PubMed
Google Scholar
Chatterjee R, Vinson C: CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression. Biochim Biophy Acta (BBA) – Gene Regul Mechan. 2012, 1819: 763-770. 10.1016/j.bbagrm.2012.02.014.
Article
CAS
Google Scholar
Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, Bird A: Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 2011, 21: 1074-1086. 10.1101/gr.118703.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y: Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010, 466: 253-257. 10.1038/nature09165.
Article
PubMed Central
CAS
PubMed
Google Scholar
Davies M, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C: Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 2012, 13: R43-10.1186/gb-2012-13-6-r43.
Article
PubMed Central
CAS
PubMed
Google Scholar
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009, 41: 178-186. 10.1038/ng.298.
Article
PubMed Central
CAS
PubMed
Google Scholar
Talens RP, Boomsma DI, Tobi EW, Kremer D, Jukema JW, Willemsen G, Putter H, Slagboom PE, Heijmans BT: Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology. FASEB J. 2010, 24: 3135-3144. 10.1096/fj.09-150490.
Article
CAS
PubMed
Google Scholar
Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F: Evaluation of the Infinium Methylation 450K technology. Epigenomics. 2011, 3: 771-784. 10.2217/epi.11.105.
Article
CAS
PubMed
Google Scholar
Roessler J, Ammerpohl O, Gutwein J, Hasemeier B, Anwar SL, Kreipe H, Lehmann U: Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina. Inc BMC Res Notes. 2012, 5: 210-10.1186/1756-0500-5-210.
Article
CAS
PubMed
Google Scholar
Thiede C, Prange-Krex G, Freiberg-Richter J, Bornhäuser M, Ehninger G: Buccal swabs but not mouthwash samples can be used to obtain pretransplant DNA fingerprints from recipients of allogeneic bone marrow transplants. Bone Marrow Transplant. 2000, 25: 575.
Article
CAS
PubMed
Google Scholar
Liu X, Yu X, Zack DJ, Zhu H, Qian J: TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinforma. 2008, 9: 271-10.1186/1471-2105-9-271.
Article
Google Scholar
Numata S, Ye T, Hyde TM, Guitart-Navarro X, Tao R, Wininger M, Colantuoni C, Weinberger DR, Kleinman JE, Lipska BK: DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet. 2012, 90: 260-272. 10.1016/j.ajhg.2011.12.020.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, et al: Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012, 337: 1190-1195. 10.1126/science.1222794.
Article
PubMed Central
CAS
PubMed
Google Scholar
The ENCODE project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489: 57-74. 10.1038/nature11247.
Article
PubMed Central
Google Scholar
Kuang YL, Paulson KE, Lichtenstein AH, Matthan NR, Lamon-Fava S: Docosahexaenoic acid suppresses apolipoprotein A-I gene expression through hepatocyte nuclear factor-3ß. Am J Clin Nutr. 2011, 94: 594-600. 10.3945/ajcn.111.012526.
Article
CAS
PubMed
Google Scholar
Gao N, LeLay J, Vatamaniuk MZ, Rieck S, Friedman JR, Kaestner KH: Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development. Genes Dev. 2008, 22: 3435-3448. 10.1101/gad.1752608.
Article
PubMed Central
CAS
PubMed
Google Scholar
Richards JB, Yuan X, Geller F, Waterworth D, Bataille V, Glass D, Song K, Waeber G, Vollenweider P, Aben KKH: Male-pattern baldness susceptibility locus at 20p11. Nat Genet. 2008, 40: 1282-1284. 10.1038/ng.255.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Hattori N, Ohgane J: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res. 2008, 18: 1969-1978. 10.1101/gr.074070.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H, Held WA: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics. 2011, 12: 231-10.1186/1471-2164-12-231.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhou Y, Lu Y, Tian W: Epigenetic features are significantly associated with alternative splicing. BMC Genomics. 2012, 13: 123-10.1186/1471-2164-13-123.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mohn F, Schübeler D: Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet. 2009, 25: 129-136. 10.1016/j.tig.2008.12.005.
Article
CAS
PubMed
Google Scholar
Wu H, Caffo B, Jaffee HA, Feinberg AP, Irizarry RA: Redefining CpG Islands using a hidden Markov model. Biostatistics. 2009, 11: 499-514.
Article
Google Scholar
Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A: CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res. 2007, 35: 6798-6807. 10.1093/nar/gkm489.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Martinez-Aroza J, Oliver JL: CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinforma. 2006, 7: 446-10.1186/1471-2105-7-446.
Article
Google Scholar
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B: The accessible chromatin landscape of the human genome. Nature. 2012, 489: 75-82. 10.1038/nature11232.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK: DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011, 480: 490-495.
CAS
PubMed
Google Scholar
Heijmans BT, Mill J: Commentary: the seven plagues of epigenetic epidemiology. Int J Epidemiol. 2012, 41: 74-78. 10.1093/ije/dyr225.
Article
PubMed Central
PubMed
Google Scholar
Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011, 12: R10-10.1186/gb-2011-12-1-r10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, et al: The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013, 45: 580-585. 10.1038/ng.2653.
Article
CAS
Google Scholar
Min JL, Lakenberg N, Bakker-Verweij M, Suchiman E, Boomsma DI, Slagboom PE, Meulenbelt I: High microsatellite and SNP genotyping success rates established in a large number of genomic DNA samples extracted from mouth swabs and genotypes. Twin Res Hum Genet. 2006, 9: 501-506. 10.1375/twin.9.4.501.
Article
PubMed
Google Scholar
Kasper Daniel Hansen and Martin Aryee: minfi: Analyze Illumina's 450k methylation arrays. R package version 1.6.0. 2012, Bioconductor
Google Scholar
Triche T: IlluminaHumanMethylation450k.db: Illumina Human Methylation 450k annotation data. R package version 1.4.7. 2012, Bioconductor
Google Scholar
Bates D, Maechler M, Bolker B: lme4: Linear mixed-effects models using S4 classes. 2012, Bioconductor
Google Scholar
Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J: The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol. 2010, 8: e1000533-10.1371/journal.pbio.1000533.
Article
PubMed Central
PubMed
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12: 996-1006.http://genome.ucsc.edu.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature. 2008, 456: 470-476. 10.1038/nature07509.
Article
PubMed Central
CAS
PubMed
Google Scholar
Koscielny G, Texier VL, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M: ASTD: the alternative splicing and transcript diversity database. Genomics. 2009, 93: 213-220. 10.1016/j.ygeno.2008.11.003.
Article
CAS
PubMed
Google Scholar
Ensembl.http://www.ensembl.org.
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G: GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010, 28: 495-501. 10.1038/nbt.1630.
Article
CAS
PubMed
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37: 1-13. 10.1093/nar/gkn923.
Article
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4: 44-57.
Article
CAS
Google Scholar
Supek F, Bosnjak M, Skunca N, Smuc T: REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011, 6: e21800-10.1371/journal.pone.0021800.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hahne F, Durinck S, Ivankek R, Mueller A, Lianoglou S: Gviz: Plotting data and annotation information along genomic coordinates. R package version 1.2.1. 2012, Bioconductor
Google Scholar
Wickham H: ggplot2: Elegant graphics for data analysis. 2009, New York: Springer
Book
Google Scholar
Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30 (1): 207-210. 10.1093/nar/30.1.207.
Article
PubMed Central
CAS
PubMed
Google Scholar