-
2
-
-
84655162785
-
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains
-
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2012;44:40-6.
-
(2012)
Nat Genet.
, vol.44
, pp. 40-46
-
-
Berman, B.P.1
Weisenberger, D.J.2
Aman, J.F.3
Hinoue, T.4
Ramjan, Z.5
Liu, Y.6
Noushmehr, H.7
Lange, C.P.8
Van Dijk, C.M.9
Tollenaar, R.A.10
-
3
-
-
80053144962
-
A decade of exploring the cancer epigenome-biological and translational implications
-
Baylin SB, Jones PA. A decade of exploring the cancer epigenome-biological and translational implications. Nat Rev Cancer. 2011;11:726-34.
-
(2011)
Nat Rev Cancer.
, vol.11
, pp. 726-734
-
-
Baylin, S.B.1
Jones, P.A.2
-
4
-
-
33644846509
-
Epigenetic gene silencing in cancer-A mechanism for early oncogenic pathway addiction?
-
Baylin SB, Ohm JE. Epigenetic gene silencing in cancer-a mechanism for early oncogenic pathway addiction? Nat Rev Cancer. 2006;6:107-16. Additional files Additional file 1: Supplementary Table S1. Excel Table Spreadsheet listing details of the constitutively unmethylated CGIs (cu-CGIs), constitutively unmethylated gene promoters (cu-GPs) and constitutively methylated gene bodies (cm-GBs). Additional file 2. Pdf document containing all Supplementary Figures S1-11, as well as Supplementary Table S2.
-
(2006)
Nat Rev Cancer.
, vol.6
, pp. 107-116
-
-
Baylin, S.B.1
Ohm, J.E.2
-
5
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43:768-75.
-
(2011)
Nat Genet.
, vol.43
, pp. 768-775
-
-
Hansen, K.D.1
Timp, W.2
Bravo, H.C.3
Sabunciyan, S.4
Langmead, B.5
McDonald, O.G.6
Wen, B.7
Wu, H.8
Liu, Y.9
Diep, D.10
-
6
-
-
59149084538
-
The human colon cancer methylome shows similar hypo-and hyper-methylation at conserved tissue-specific CpG island shores
-
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. The human colon cancer methylome shows similar hypo-and hyper-methylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41:178-86.
-
(2009)
Nat Genet.
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Wen, B.3
Wu, Z.4
Montano, C.5
Onyango, P.6
Cui, H.7
Gabo, K.8
Rongione, M.9
Webster, M.10
-
7
-
-
84893711405
-
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization
-
Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res. 2014;24:177-84.
-
(2014)
Genome Res.
, vol.24
, pp. 177-184
-
-
Hansen, K.D.1
Sabunciyan, S.2
Langmead, B.3
Nagy, N.4
Curley, R.5
Klein, G.6
Klein, E.7
Salamon, D.8
Feinberg, A.P.9
-
8
-
-
84906837231
-
Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors
-
Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 2014;6(8):61.
-
(2014)
Genome Med.
, vol.6
, Issue.8
, pp. 61
-
-
Timp, W.1
Bravo, H.C.2
McDonald, O.G.3
Goggins, M.4
Umbricht, C.5
Zeiger, M.6
Feinberg, A.P.7
Irizarry, R.A.8
-
9
-
-
84655162785
-
Regions of focal DNA hypermethylation and long range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains
-
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CPE, van Dijk CM, Tollenar RA, et al. Regions of focal DNA hypermethylation and long range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011;44(1):40-6.
-
(2011)
Nat Genet.
, vol.44
, Issue.1
, pp. 40-46
-
-
Berman, B.P.1
Weisenberger, D.J.2
Aman, J.F.3
Hinoue, T.4
Ramjan, Z.5
Liu, Y.6
Noushmehr, H.7
Lange, C.P.E.8
Van Dijk, C.M.9
Tollenar, R.A.10
-
10
-
-
59149083658
-
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
-
Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet. 2009;41:246-50.
-
(2009)
Nat Genet.
, vol.41
, pp. 246-250
-
-
Wen, B.1
Wu, H.2
Shinkai, Y.3
Irizarry, R.A.4
Feinberg, A.P.5
-
11
-
-
33846576622
-
Epigenetic stem cell signature in cancer
-
Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, Laird PW. Epigenetic stem cell signature in cancer. Nat Genet. 2007;39:157-8.
-
(2007)
Nat Genet.
, vol.39
, pp. 157-158
-
-
Widschwendter, M.1
Fiegl, H.2
Egle, D.3
Mueller-Holzner, E.4
Spizzo, G.5
Marth, C.6
Weisenberger, D.J.7
Campan, M.8
Young, J.9
Jacobs, I.10
Laird, P.W.11
-
12
-
-
33846649587
-
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer
-
Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E, Yakhini Z, Ben-Shushan E, Reubinoff BE, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet. 2007;39:232-6.
-
(2007)
Nat Genet.
, vol.39
, pp. 232-236
-
-
Schlesinger, Y.1
Straussman, R.2
Keshet, I.3
Farkash, S.4
Hecht, M.5
Zimmerman, J.6
Eden, E.7
Yakhini, Z.8
Ben-Shushan, E.9
Reubinoff, B.E.10
-
13
-
-
33846569960
-
A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing
-
Ohm JE, McGarvey KM, Yu X, Cheng L, Schuebel KE, Cope L, Mohammad HP, Chen W, Daniel VC, Yu W, et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet. 2007;39:237-42.
-
(2007)
Nat Genet.
, vol.39
, pp. 237-242
-
-
Ohm, J.E.1
McGarvey, K.M.2
Yu, X.3
Cheng, L.4
Schuebel, K.E.5
Cope, L.6
Mohammad, H.P.7
Chen, W.8
Daniel, V.C.9
Yu, W.10
-
14
-
-
84924407381
-
An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging
-
Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet. 2015;11:e1004996.
-
(2015)
PLoS Genet.
, vol.11
, pp. e1004996
-
-
Yuan, T.1
Jiao, Y.2
De Jong, S.3
Ophoff, R.A.4
Beck, S.5
Teschendorff, A.E.6
-
15
-
-
77950650405
-
Agedependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
-
Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, et al. Agedependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 2010;20:440-6.
-
(2010)
Genome Res.
, vol.20
, pp. 440-446
-
-
Teschendorff, A.E.1
Menon, U.2
Gentry-Maharaj, A.3
Ramus, S.J.4
Weisenberger, D.J.5
Shen, H.6
Campan, M.7
Noushmehr, H.8
Bell, C.G.9
Maxwell, A.P.10
-
16
-
-
84896501999
-
Molecular rules governing de novo methylation in cancer
-
Nejman D, Straussman R, Steinfeld I, Ruvolo M, Roberts D, Yakhini Z, Cedar H. Molecular rules governing de novo methylation in cancer. Cancer Res. 2014;74:1475-83.
-
(2014)
Cancer Res.
, vol.74
, pp. 1475-1483
-
-
Nejman, D.1
Straussman, R.2
Steinfeld, I.3
Ruvolo, M.4
Roberts, D.5
Yakhini, Z.6
Cedar, H.7
-
17
-
-
84866844032
-
Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
-
Sproul D, Kitchen RR, Nestor CE, Dixon JM, Sims AH, Harrison DJ, Ramsahoye BH, Meehan RR. Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol. 2012;13:R84.
-
(2012)
Genome Biol.
, vol.13
, pp. R84
-
-
Sproul, D.1
Kitchen, R.R.2
Nestor, C.E.3
Dixon, J.M.4
Sims, A.H.5
Harrison, D.J.6
Ramsahoye, B.H.7
Meehan, R.R.8
-
18
-
-
79952716583
-
Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer
-
Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH. Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci USA. 2011;108:4364-9.
-
(2011)
Proc Natl Acad Sci USA.
, vol.108
, pp. 4364-4369
-
-
Sproul, D.1
Nestor, C.2
Culley, J.3
Dickson, J.H.4
Dixon, J.M.5
Harrison, D.J.6
Meehan, R.R.7
Sims, A.H.8
Ramsahoye, B.H.9
-
19
-
-
84923358817
-
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
-
Polak P, Karlic R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahovicek K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 2015;518:360-4.
-
(2015)
Nature.
, vol.518
, pp. 360-364
-
-
Polak, P.1
Karlic, R.2
Koren, A.3
Thurman, R.4
Sandstrom, R.5
Lawrence, M.S.6
Reynolds, A.7
Rynes, E.8
Vlahovicek, K.9
Stamatoyannopoulos, J.A.10
Sunyaev, S.R.11
-
20
-
-
77649240380
-
Widespread and tissue specific age-related DNA methylation changes in mice
-
Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, Zhang N, Liang S, Donehower LA, Issa JP. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010;20:332-40.
-
(2010)
Genome Res.
, vol.20
, pp. 332-340
-
-
Maegawa, S.1
Hinkal, G.2
Kim, H.S.3
Shen, L.4
Zhang, L.5
Zhang, J.6
Zhang, N.7
Liang, S.8
Donehower, L.A.9
Issa, J.P.10
-
21
-
-
77950657253
-
Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
-
Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 2010;20:434-9.
-
(2010)
Genome Res.
, vol.20
, pp. 434-439
-
-
Rakyan, V.K.1
Down, T.A.2
Maslau, S.3
Andrew, T.4
Yang, T.P.5
Beyan, H.6
Whittaker, P.7
McCann, O.T.8
Finer, S.9
Valdes, A.M.10
-
22
-
-
84860643156
-
Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives
-
Nazor KL, Altun G, Lynch C, Tran H, Harness JV, Slavin I, Garitaonandia I, Muller FJ, Wang YC, Boscolo FS, et al. Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. Cell Stem Cell. 2012;10:620-34.
-
(2012)
Cell Stem Cell.
, vol.10
, pp. 620-634
-
-
Nazor, K.L.1
Altun, G.2
Lynch, C.3
Tran, H.4
Harness, J.V.5
Slavin, I.6
Garitaonandia, I.7
Muller, F.J.8
Wang, Y.C.9
Boscolo, F.S.10
-
23
-
-
79958754527
-
Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome
-
Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome. Epigenetics. 2011;6:692-702.
-
(2011)
Epigenetics.
, vol.6
, pp. 692-702
-
-
Sandoval, J.1
Heyn, H.2
Moran, S.3
Serra-Musach, J.4
Pujana, M.A.5
Bibikova, M.6
Esteller, M.7
-
24
-
-
84865248380
-
Chromatin organization is a major influence on regional mutation rates in human cancer cells
-
Schuster-Bockler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012;488:504-7.
-
(2012)
Nature.
, vol.488
, pp. 504-507
-
-
Schuster-Bockler, B.1
Lehner, B.2
-
25
-
-
84939178416
-
An integrative pancancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer
-
Yang Z, Jones A, Widschwendter M, Teschendorff AE. An integrative pancancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer. Genome Biol. 2015;16:140.
-
(2015)
Genome Biol.
, vol.16
, pp. 140
-
-
Yang, Z.1
Jones, A.2
Widschwendter, M.3
Teschendorff, A.E.4
-
26
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518:317-30.
-
(2015)
Nature.
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
Kheradpour, P.7
Zhang, Z.8
Wang, J.9
-
27
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489:75-82.
-
(2012)
Nature.
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
Sheffield, N.C.7
Stergachis, A.B.8
Wang, H.9
Vernot, B.10
-
28
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics. 2001;17:520-5.
-
(2001)
Bioinformatics.
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
Tibshirani, R.6
Botstein, D.7
Altman, R.B.8
-
29
-
-
84872564830
-
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450k DNA methylation data
-
Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450k DNA methylation data. Bioinformatics. 2013;29:189-96.
-
(2013)
Bioinformatics.
, vol.29
, pp. 189-196
-
-
Teschendorff, A.E.1
Marabita, F.2
Lechner, M.3
Bartlett, T.4
Tegner, J.5
Gomez-Cabrero, D.6
Beck, S.7
-
30
-
-
77949533111
-
An epigenetic signature in peripheral blood predicts active ovarian cancer
-
Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, Widschwendter M. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One. 2009;4:e8274.
-
(2009)
PLoS One.
, vol.4
, pp. e8274
-
-
Teschendorff, A.E.1
Menon, U.2
Gentry-Maharaj, A.3
Ramus, S.J.4
Gayther, S.A.5
Apostolidou, S.6
Jones, A.7
Lechner, M.8
Beck, S.9
Jacobs, I.J.10
Widschwendter, M.11
|