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BioMed Research International
Volume 2013 (2013), Article ID 709042, 6 pages
CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands
1Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
2Laboratório de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, 18100 Granada, Spain
Received 20 April 2013; Revised 12 July 2013; Accepted 19 August 2013
Academic Editor: Stephan Koblmüller
Copyright © 2013 Guillermo Barturen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. Bird, “DNA methylation patterns and epigenetic memory,” Genes and Development, vol. 16, no. 1, pp. 6–21, 2002.
- A. P. Bird, “CpG-rich islands and the function of DNA methylation,” Nature, vol. 321, no. 6067, pp. 209–213, 1986.
- D. Schubeler, “Molecular biology. Epigenetic islands in a genetic ocean,” Science, vol. 338, no. 6108, pp. 756–757, 2012.
- J. Zhu, F. He, S. Hu, and J. Yu, “On the nature of human housekeeping genes,” Trends in Genetics, vol. 24, no. 10, pp. 481–484, 2008.
- S. B. Baylin, M. Esteller, M. R. Rountree, K. E. Bachman, K. Schuebel, and J. G. Herman, “Abberant patterns of DNA methylation, chromatin formation and gene expression in cancer,” Human Molecular Genetics, vol. 10, no. 7, pp. 687–692, 2001.
- C. de Smet, C. Lurquin, B. Lethé, V. Martelange, and T. Boon, “DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter,” Molecular and Cellular Biology, vol. 19, no. 11, pp. 7327–7335, 1999.
- M. Esteller, P. G. Corn, S. B. Baylin, and J. G. Herman, “A gene hypermethylation profile of human cancer,” Cancer Research, vol. 61, no. 8, pp. 3225–3229, 2001.
- J.-P. Issa, “CpG island methylator phenotype in cancer,” Nature Reviews Cancer, vol. 4, no. 12, pp. 988–993, 2004.
- Y. Riazalhosseini and J. D. Hoheisel, “Do we use the appropriate controls for the identification of informative methylation markers for early cancer detection?” Genome Biology, vol. 9, no. 11, article 405, 2008.
- A. R. Krebs and D. Schubeler, “Tracking the evolution of cancer methylomes,” Nature Genetics, vol. 44, no. 11, pp. 1173–1174, 2012.
- J. Zeng, G. Konopka, B. G. Hunt, T. M. Preuss, D. Geschwind, and S. V. Yi, “Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution,” The American Journal of Human Genetics, vol. 91, no. 3, pp. 455–465, 2012.
- C. G. Bell, G. A. Wilson, L. M. Butcher, C. Roos, L. Walter, and S. Beck, “Human-specific CpG, “beacons” identify loci associated with human-specific traits and disease,” Epigenetics, vol. 7, no. 10, pp. 1188–1199, 2012.
- V. Negre and C. Grunau, “The MethDB DAS server: adding an epigenetic information layer to the human genome,” Epigenetics, vol. 1, no. 2, pp. 101–105, 2006.
- J. Shi, J. Hu, Q. Zhou, Y. Du, and C. Jiang, “PEpiD: a prostate epigenetic database in mammals,” PLoS One, vol. 8, no. 5, Article ID e64289, 2013.
- F. Gu, M. S. Doderer, Y.-W. Huang, et al., “CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers,” PLoS One, vol. 8, no. 4, Article ID e60980, 2013.
- H.-C. Kuo, P.-Y. Lin, T.-C. Chung et al., “DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells,” Journal of Computational Biology, vol. 18, no. 8, pp. 1013–1017, 2011.
- B. Aissani and G. Bernardi, “CpG islands, genes and isochores in the genomes of vertebrates,” Gene, vol. 106, no. 2, pp. 185–195, 1991.
- K. Jabbari and G. Bernardi, “CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families,” Gene, vol. 224, no. 1-2, pp. 123–128, 1998.
- N. M. Cohen, E. Kenigsberg, and A. Tanay, “Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection,” Cell, vol. 145, no. 5, pp. 773–786, 2011.
- D. Karolchik, R. M. Kuhn, R. Baertsch et al., “The UCSC genome browser database: 2008 update,” Nucleic Acids Research, vol. 36, no. 1, pp. D773–D779, 2008.
- M. Hackenberg, P. Carpena, P. Bernaola-Galván, G. Barturen, Á. M. Alganza, and J. L. Oliver, “WordCluster: detecting clusters of DNA words and genomic elements,” Algorithms for Molecular Biology, vol. 6, no. 1, article 2, 2011.
- M. Hackenberg, C. Previti, P. L. Luque-Escamilla, P. Carpena, J. Martínez-Aroza, and J. L. Oliver, “CpGcluster: a distance-based algorithm for CpG-island detection,” BMC Bioinformatics, vol. 7, article 446, 2006.
- D. Takai and P. A. Jones, “The CpG island searcher: a new WWW resource,” In Silico Biology, vol. 3, no. 3, pp. 235–240, 2003.
- M. Weber, I. Hellmann, M. B. Stadler et al., “Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome,” Nature Genetics, vol. 39, no. 4, pp. 457–466, 2007.
- R. Illingworth, A. Kerr, D. Desousa et al., “A novel CpG island set identifies tissue-specific methylation at developmental gene loci,” PLoS Biology, vol. 6, no. 1, article e22, 2008.
- R. M. Waterhouse, E. M. Zdobnov, F. Tegenfeldt, J. Li, and E. V. Kriventseva, “OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011,” Nucleic Acids Research, vol. 39, no. 1, pp. D283–D288, 2011.
- T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981.
- B. Giardine, C. Riemer, R. C. Hardison et al., “Galaxy: a platform for interactive large-scale genome analysis,” Genome Research, vol. 15, no. 10, pp. 1451–1455, 2005.
- J. Goecks, A. Nekrutenko, and J. Taylor, “Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences,” Genome Biology, vol. 11, no. 8, article R86, 2010.
- R. S. Illingworth and A. P. Bird, “CpG islands—‘a rough guide’,” FEBS Letters, vol. 583, no. 11, pp. 1713–1720, 2009.
- M. Hackenberg, G. Barturen, and J. L. Oliver, “NGSmethDB: a database for next-generation sequencing single-cytosine- resolution DNAmethylation data,” Nucleic Acids Research, vol. 39, no. 1, pp. D75–D79, 2011.
- S. Geisen, et al., “NGSmethDB: high-quality, single-cytosine resolution methylation maps,” submitted to Nucleic Acids Research.
- M. Hackenberg, G. Barturen, and J. L. Oliver, “Methylation profiling from high-throughput sequencing data,” in DNA Methylation—From Genomics to Technology, T. Tatarinova and O. Kerton, Eds., p. 27, In-Tech, 2012.
- G. Barturen, A. Rueda, J. L. Oliver, and M. Hackenberg, “MethylExtract: high-quality methylation maps and SNV calling from whole genome bisulfite sequencing data,” submitted.
- K. A. Gray, L. C. Daugherty, S. M. Gordon, R. L. Seal, M. W. Wright, and E. A. Bruford, “Genenames.org: the HGNC resources in 2013,” Nucleic Acids Research, vol. 41, pp. D545–D552, 2013.
- A. Kasprzyk, “BioMart: driving a paradigm change in biological data management,” Database, vol. 2011, article bar049, 2011.
- M. E. Skinner and I. H. Holmes, “Setting up the JBrowse genome browser,” Current Protocols in Bioinformatics, chapter 9, p. unit 9.13, 2010.
- M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes, “JBrowse: a next-generation genome browser,” Genome Research, vol. 19, no. 9, pp. 1630–1638, 2009.
- M. Hackenberg, G. Barturen, P. Carpena, P. L. Luque-Escamilla, C. Previti, and J. L. Oliver, “Prediction of CpG-island function: CpG clustering vs. sliding-window methods,” BMC Genomics, vol. 11, no. 1, article 327, 2010.
- T. J. Hubbard, B. L. Aken, S. Ayling, et al., “Ensembl 2009,” Nucleic Acids Research, vol. 37, database issue, pp. D690–D697, 2009.