Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

References

• Ferlay J, Shin H-R, Bray F, Forman D, Mathers C, Parkin DM. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 2010; 127:2893 - 917; http://dx.doi.org/10.1002/ijc.25516; PMID: 21351269
   PubMed Web of Science ®Google Scholar
• Laird PW. Cancer epigenetics. Hum Mol Genet 2005; 14:Spec No 1 R65 - 76; http://dx.doi.org/10.1093/hmg/ddi113; PMID: 15809275
   PubMed Web of Science ®Google Scholar
• Issa J-P. CpG island methylator phenotype in cancer. Nat Rev Cancer 2004; 4:988 - 93; http://dx.doi.org/10.1038/nrc1507; PMID: 15573120
   PubMed Web of Science ®Google Scholar
• Rashid A, Issa J-PJ. CpG island methylation in gastroenterologic neoplasia: a maturing field. Gastroenterology 2004; 127:1578 - 88; http://dx.doi.org/10.1053/j.gastro.2004.09.007; PMID: 15521024
   PubMed Web of Science ®Google Scholar
• Hinoue T, Weisenberger DJ, Lange CPE, Shen H, Byun HM, Van Den Berg D, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012; 22:271 - 82; http://dx.doi.org/10.1101/gr.117523.110; PMID: 21659424
   PubMed Web of Science ®Google Scholar
• Xu Y, Hu B, Choi AJ, Gopalan B, Lee BH, Kalady MF, et al. Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. Genome Res 2012; 22:283 - 91; http://dx.doi.org/10.1101/gr.122788.111; PMID: 21990380
   PubMed Web of Science ®Google Scholar
• Kober P, Bujko M, Olędzki J, Tysarowski A, Siedlecki JA. Methyl-CpG binding column-based identification of nine genes hypermethylated in colorectal cancer. Mol Carcinog 2011; 50:846 - 56; http://dx.doi.org/10.1002/mc.20763; PMID: 21438024
   PubMed Web of Science ®Google Scholar
• Øster B, Thorsen K, Lamy P, Wojdacz TK, Hansen LL, Birkenkamp-Demtröder K, et al. Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int J Cancer 2011; 129:2855 - 66; http://dx.doi.org/10.1002/ijc.25951; PMID: 21400501
   PubMed Web of Science ®Google Scholar
• Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods 2010; 52:232 - 6; http://dx.doi.org/10.1016/j.ymeth.2010.06.012; PMID: 20542119
   PubMed Web of Science ®Google Scholar
• Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010; 28:1106 - 14; http://dx.doi.org/10.1038/nbt.1681; PMID: 20852634
   PubMed Web of Science ®Google Scholar
• Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, et al. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res 2011; 21:1313 - 27; http://dx.doi.org/10.1101/gr.114843.110; PMID: 21636662
   PubMed Web of Science ®Google Scholar
• Brinkman AB, Gu H, Bartels SJJ, Zhang Y, Matarese F, Simmer F, et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 2012; 22:1128 - 38; http://dx.doi.org/10.1101/gr.133728.111; PMID: 22466170
   PubMed Web of Science ®Google Scholar
• Friedman J, Hastie T, Tibshirani R. Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw 2010; 33:1 - 22; PMID: 20808728
   PubMed Web of Science ®Google Scholar
• Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006; 38:787 - 93; http://dx.doi.org/10.1038/ng1834; PMID: 16804544
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008; 4:44 - 57; http://dx.doi.org/10.1038/nprot.2008.211
   PubMed Web of Science ®Google Scholar
• Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37:1 - 13; http://dx.doi.org/10.1093/nar/gkn923; PMID: 19033363
   PubMed Web of Science ®Google Scholar
• Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res 2012; 22:407 - 19; http://dx.doi.org/10.1101/gr.119867.110; PMID: 21613409
   PubMed Web of Science ®Google Scholar
• Essner JJ, Chen E, Ekker SC. Syndecan-2. Int J Biochem Cell Biol 2006; 38:152 - 6; http://dx.doi.org/10.1016/j.biocel.2005.08.012; PMID: 16198615
   PubMed Web of Science ®Google Scholar
• Hatano M, Roberts CW, Minden M, Crist WM, Korsmeyer SJ. Deregulation of a homeobox gene, HOX11, by the t(10;14) in T cell leukemia. Science 1991; 253:79 - 82; http://dx.doi.org/10.1126/science.1676542; PMID: 1676542
   PubMed Web of Science ®Google Scholar
• Dear TN, Colledge WH, Carlton MB, Lavenir I, Larson T, Smith AJ, et al. The Hox11 gene is essential for cell survival during spleen development. Development 1995; 121:2909 - 15; PMID: 7555717
   PubMed Web of Science ®Google Scholar
• Qian Y, Shirasawa S, Chen CL, Cheng L, Ma Q. Proper development of relay somatic sensory neurons and D2/D4 interneurons requires homeobox genes Rnx/Tlx-3 and Tlx-1. Genes Dev 2002; 16:1220 - 33; http://dx.doi.org/10.1101/gad.982802; PMID: 12023301
   PubMed Web of Science ®Google Scholar
• Rhee I, Bachman KE, Park BH, Jair K-W, Yen R-WC, Schuebel KE, et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 2002; 416:552 - 6; http://dx.doi.org/10.1038/416552a; PMID: 11932749
   PubMed Web of Science ®Google Scholar
• ENCODE Project Consortium. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011; 9:e1001046; http://dx.doi.org/10.1371/journal.pbio.1001046; PMID: 21526222
   PubMed Web of Science ®Google Scholar
• Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125:315 - 26; http://dx.doi.org/10.1016/j.cell.2006.02.041; PMID: 16630819
   PubMed Web of Science ®Google Scholar
• Shu W, Chen H, Bo X, Wang S. Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res 2011; 39:7428 - 43; http://dx.doi.org/10.1093/nar/gkr443; PMID: 21685456
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137; http://dx.doi.org/10.1186/gb-2008-9-9-r137; PMID: 18798982
   PubMed Web of Science ®Google Scholar
• Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 2011; 71:6320 - 6; http://dx.doi.org/10.1158/0008-5472.CAN-11-1021; PMID: 21862635
   PubMed Web of Science ®Google Scholar
• Baylin SB, Ohm JE. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?. Nat Rev Cancer 2006; 6:107 - 16; http://dx.doi.org/10.1038/nrc1799; PMID: 16491070
   PubMed Web of Science ®Google Scholar
• Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983; 301:89 - 92; http://dx.doi.org/10.1038/301089a0; PMID: 6185846
   PubMed Web of Science ®Google Scholar
• Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, et al. The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 1983; 11:6883 - 94; http://dx.doi.org/10.1093/nar/11.19.6883; PMID: 6314264
   PubMed Web of Science ®Google Scholar
• Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene 2002; 21:5400 - 13; http://dx.doi.org/10.1038/sj.onc.1205651; PMID: 12154403
   PubMed Web of Science ®Google Scholar
• Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006; 125:301 - 13; http://dx.doi.org/10.1016/j.cell.2006.02.043; PMID: 16630818
   PubMed Web of Science ®Google Scholar
• Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006; 38:149 - 53; http://dx.doi.org/10.1038/ng1719; PMID: 16444255
   PubMed Web of Science ®Google Scholar
• Easwaran H, Johnstone SE, Van Neste L, Ohm J, Mosbruger T, Wang Q, et al. A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res 2012; 22:837 - 49; http://dx.doi.org/10.1101/gr.131169.111; PMID: 22391556
   PubMed Web of Science ®Google Scholar
• Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, et al. Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci U S A 2011; 108:4364 - 9; http://dx.doi.org/10.1073/pnas.1013224108; PMID: 21368160
   PubMed Web of Science ®Google Scholar
• Huang X, Xiao D-W, Xu L-Y, Zhong H-J, Liao L-D, Xie Z-F, et al. Prognostic significance of altered expression of SDC2 and CYR61 in esophageal squamous cell carcinoma. Oncol Rep 2009; 21:1123 - 9; PMID: 19288017
   PubMed Web of Science ®Google Scholar
• Popović A, Demirović A, Spajić B, Stimac G, Kruslin B, Tomas D. Expression and prognostic role of syndecan-2 in prostate cancer. Prostate Cancer Prostatic Dis 2010; 13:78 - 82; http://dx.doi.org/10.1038/pcan.2009.43; PMID: 19786981
   PubMed Web of Science ®Google Scholar
• Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005; 21:4067 - 8; http://dx.doi.org/10.1093/bioinformatics/bti652; PMID: 16141249
   PubMed Web of Science ®Google Scholar
• Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, et al. Identification of novel functional TBP-binding sites and general factor repertoires. EMBO J 2007; 26:944 - 54; http://dx.doi.org/10.1038/sj.emboj.7601550; PMID: 17268553
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Ladd-Acosta C, Wen B, Wu A, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41:178 - 86
   PubMed Web of Science ®Google Scholar
• Karpinski P, Ramsey D, Grzenieniak Z, Sasiadek MM, Blin N. The CpG island methylator phenotype correlates with long-range epigenetic silencing in the colorectal cancer. Molecular Cancer Research 2008; 6:585 - 91
   PubMed Web of Science ®Google Scholar