參考文獻 |
[1] B. E. Stranger, M. S. Forrest, M. Dunning, C. E. Ingle, C. Beazley, N. Thorne, et al., "Relative impact of nucleotide and copy number variation on gene expression phenotypes," Science, vol. 315, pp. 848-53, Feb 9 2007.
[2] L. Han, B. Su, W. H. Li, and Z. Zhao, "CpG island density and its correlations with genomic features in mammalian genomes," Genome Biol, vol. 9, p. R79, 2008.
[3] A. Hermann, R. Goyal, and A. Jeltsch, "The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites," J Biol Chem, vol. 279, pp. 48350-9, Nov 12 2004.
[4] R. J. Klose and A. P. Bird, "Genomic DNA methylation: the mark and its mediators," Trends Biochem Sci, vol. 31, pp. 89-97, Feb 2006.
[5] K. D. Robertson and A. P. Wolffe, "DNA methylation in health and disease," Nat Rev Genet, vol. 1, pp. 11-9, Oct 2000.
[6] R. E. Amir, I. B. Van den Veyver, M. Wan, C. Q. Tran, U. Francke, and H. Y. Zoghbi, "Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2," Nature Genetics, vol. 23, pp. 185-188, Oct 1999.
[7] M. Esteller, J. M. Silva, G. Dominguez, F. Bonilla, X. Matias-Guiu, E. Lerma, et al., "Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors," J Natl Cancer Inst, vol. 92, pp. 564-9, Apr 5 2000.
[8] P. A.Marks, "," Nature Reviews Cancer vol. 1, pp. 194-202, 2001.
[9] V. W. Zhou, A. Goren, and B. E. Bernstein, "Charting histone modifications and the functional organization of mammalian genomes," Nat Rev Genet, vol. 12, pp. 7-18, Jan 2011.
[10] G. Sadri-Vakili and J. H. Cha, "Mechanisms of disease: Histone modifications in Huntington’s disease," Nat Clin Pract Neurol, vol. 2, pp. 330-8, Jun 2006.
[11] S. R. Bhaumik, E. Smith, and A. Shilatifard, "Covalent modifications of histones during development and disease pathogenesis," Nat Struct Mol Biol, vol. 14, pp. 1008-16, Nov 2007.
[12] O. F. Sarmento, L. C. Digilio, Y. Wang, J. Perlin, J. C. Herr, C. D. Allis, et al., "Dynamic alterations of specific histone modifications during early murine development," J Cell Sci, vol. 117, pp. 4449-59, Sep 1 2004.
[13] E. Hinde, F. Cardarelli, A. Chen, M. Khine, and E. Gratton, "Tracking the mechanical dynamics of human embryonic stem cell chromatin," Epigenetics Chromatin, vol. 5, p. 20, 2012.
[14] P. A. Jones and S. B. Baylin, "The epigenomics of cancer," Cell, vol. 128, pp. 683-92, Feb 23 2007.
[15] Y. Kondo and J.-P. J. Issa, "Epigenetic changes in colorectal cance," Cancer and Metastasis Reviews, vol. 23, pp. 29-39, 2004.
[16] X. Jiang, J. Tan, J. Li, S. Kivimae, X. Yang, L. Zhuang, et al., "DACT3 is an epigenetic regulator of Wnt/beta-catenin signaling in colorectal cancer and is a therapeutic target of histone modifications," Cancer Cell, vol. 13, pp. 529-41, Jun 2008.
[17] R. E. Thurman, E. Rynes, R. Humbert, J. Vierstra, M. T. Maurano, E. Haugen, et al., "The accessible chromatin landscape of the human genome," Nature, vol. 489, pp. 75-82, Sep 6 2012.
[18] X. Dong, M. C. Greven, A. Kundaje, S. Djebali, J. B. Brown, C. Cheng, et al., "Modeling gene expression using chromatin features in various cellular contexts," Genome Biol, vol. 13, p. R53, 2012.
[19] C. M. Koch, R. M. Andrews, P. Flicek, S. C. Dillon, U. Karaoz, G. K. Clelland, et al., "The landscape of histone modifications across 1% of the human genome in five human cell lines," Genome Res, vol. 17, pp. 691-707, Jun 2007.
[20] A. Barski, S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones, Z. Wang, et al., "High-resolution profiling of histone methylations in the human genome," Cell, vol. 129, pp. 823-37, May 18 2007.
[21] D. J. Steger, M. I. Lefterova, L. Ying, A. J. Stonestrom, M. Schupp, D. Zhuo, et al., "DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells," Mol Cell Biol, vol. 28, pp. 2825-39, Apr 2008.
[22] P. Madrigal and P. Krajewski, "Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data," Front Genet, vol. 3, p. 230, 2012.
[23] T. S. Mikkelsen, M. Ku, D. B. Jaffe, B. Issac, E. Lieberman, G. Giannoukos, et al., "Genome-wide maps of chromatin state in pluripotent and lineage-committed cells," Nature, vol. 448, pp. 553-60, Aug 2 2007.
[24] C. Gene Ontology, "The Gene Ontology project in 2008," Nucleic Acids Res, vol. 36, pp. D440-4, Jan 2008.
[25] C. J. Mungall, M. Bada, T. Z. Berardini, J. Deegan, A. Ireland, M. A. Harris, et al., "Cross-product extensions of the Gene Ontology," J Biomed Inform, vol. 44, pp. 80-6, Feb 2011.
[26] E. Eden, R. Navon, I. Steinfeld, D. Lipson, and Z. Yakhini, "GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists," BMC Bioinformatics, vol. 10, p. 48, 2009.
[27] J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, et al., "GENCODE: the reference human genome annotation for The ENCODE Project," Genome Res, vol. 22, pp. 1760-74, Sep 2012.
[28] G. Pan, S. Tian, J. Nie, C. Yang, V. Ruotti, H. Wei, et al., "Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells," Cell Stem Cell, vol. 1, pp. 299-312, Sep 13 2007.
[29] D. L. Jones and A. J. Wagers, "No place like home: anatomy and function of the stem cell niche," Nat Rev Mol Cell Biol, vol. 9, pp. 11-21, Jan 2008.
[30] P. Chi, C. D. Allis, and G. G. Wang, "Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers," Nat Rev Cancer, vol. 10, pp. 457-69, Jul 2010.
[31] X.-S. Ke, "Genome-Wide Profiling of Histone H3 Lysine 4 and Lysine 27 Trimethylation Reveals an Epigenetic Signature in Prostate Carcinogenesis.," PLoS ONE, vol. 4, pp. 1-14, 2009.
[32] T. Miki, T. Lehmann, H. Cai, D. B. Stolz, and S. C. Strom, "Stem cell characteristics of amniotic epithelial cells," Stem Cells, vol. 23, pp. 1549-59, Nov-Dec 2005.
[33] K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda, et al., "Induction of pluripotent stem cells from adult human fibroblasts by defined factors," Cell, vol. 131, pp. 861-72, Nov 30 2007.
[34] S. Yamanaka, "A fresh look at iPS cells," Cell, vol. 137, pp. 13-7, Apr 3 2009.
[35] T. E. P. Consortium, "A User’s Guide to the Encyclopedia of DNA Elements (ENCODE),"
PLOS BIOLOGY, vol. 9, 20
[36] P. J. Sabo, M. S. Kuehn, R. Thurman, B. E. Johnson, E. M. Johnson, H. Cao, et al., "Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays," Nat Methods, vol. 3, pp. 511-8, Jul 2006.
[37] S. G. Landt, G. K. Marinov, A. Kundaje, P. Kheradpour, F. Pauli, S. Batzoglou, et al., "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia," Genome Res, vol. 22, pp. 1813-31, Sep 2012. |