GBSA: A comprehensive software for analysing whole genome bisulfite sequencing data

Nucleic Acids Research

Volumn 41, Issue 4, 2013, Pages

  Benoukraf, Touati ^a   Wongphayak, Sarawut ^a   Hadi, Luqman Hakim Abdul ^a   Wu, Mengchu ^a   Soong, Richie ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; DNA; RNA; SPACER DNA;

ARTICLE; CAT; DATA ANALYSIS SOFTWARE; DNA METHYLATION; GENE CONTROL; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; INFORMATION PROCESSING; NONHUMAN; ONLINE SYSTEM; PLANT; PRIORITY JOURNAL; QUALITY CONTROL; REGULATORY MECHANISM; RNA SEQUENCE; SCORING SYSTEM; SEQUENCE ANALYSIS; STEM CELL;

DNA METHYLATION; GENOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES; TRANSCRIPTION INITIATION SITE;

EID: 84876387793     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1281     Document Type: Article

References (40)

1. Feinberg, A.P. (2007) Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433-440.
2. Laird, P.W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
3. Ruike, Y., Imanaka, Y., Sato, F., Shimizu, K. and Tsujimoto, G. (2010) Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics, 11, 137.
4. Serre, D., Lee, B.H. and Ting, A.H. (2010) MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res., 38, 391-399.
5. Brinkman, A.B., Simmer, F., Ma, K., Kaan, A., Zhu, J. and Stunnenberg, H.G. (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods, 52, 232-236.
6. Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. and Ecker, J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
7. Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M. and Jacobsen, S.E. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219.
8. Meissner, A., Gnirke, A., Bell, G.W., Ramsahoye, B., Lander, E.S. and Jaenisch, R. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res., 33, 5868-5877.
9. Meissner, A., Mikkelsen, T.S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B.E., Nusbaum, C., Jaffe, D.B. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770.
10. Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J. and Lengauer, T. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics, 21, 4067-4068.
11. Xu, Y.H., Manoharan, H.T. and Pitot, H.C. (2007) CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA. Biotechniques, 43, 334, 336-340, 342.
12. Kumaki, Y., Oda, M. and Okano, M. (2008) QUMA: quantification tool for methylation analysis. Nucleic Acids Res., 36, W170-W175.
13. Rohde, C., Zhang, Y., Reinhardt, R. and Jeltsch, A. (2010) BISMA-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics, 11, 230.
14. Pedersen, B., Hsieh, T.-F., Ibarra, C. and Fischer, R.L. (2011) MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics, 27, 2435-2436.
15. Lutsik, P., Feuerbach, L., Arand, J., Lengauer, T., Walter, J. and Bock, C. (2011) BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res., 39, W551-W556.
16. Wu, T.D. and Watanabe, C.K. (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.
17. Krueger, F. and Andrews, S.R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
18. Xi, Y. and Li, W. (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics, 10, 232.
19. Chen, P.Y., Cokus, S.J. and Pellegrini, M. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.
20. Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A. and Li, W. (2011) RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics, 28, 430-432.
21. Krueger, F., Kreck, B., Franke, A. and Andrews, S.R. (2012) DNA methylome analysis using short bisulfite sequencing data. Nat. Methods, 9, 145-151.
22. Lister, R., Pelizzola, M., Kida, Y.S., Hawkins, R.D., Nery, J.R., Hon, G., Antosiewicz-Bourget, J., O'Malley, R., Castanon, R., Klugman, S. et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 470, 68-73.
23. Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. and Loraine, A.E. (2009) The integrated genome browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics, 25, 2730-2731.
24. Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G. and Mesirov, J.P. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26.
25. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
26. Brenet, F., Moh, M., Funk, P., Feierstein, E., Viale, A.J., Socci, N.D. and Scandura, J.M. (2011) DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One, 6, e14524.
27. Hodges, E., Molaro, A., Dos Santos, C.O., Thekkat, P., Song, Q., Uren, P.J., Park, J., Butler, J., Rafii, S., McCombie, W.R. et al. (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell, 44, 17-28.
28. Li, Y., Zhu, J., Tian, G., Li, N., Li, Q., Ye, M., Zheng, H., Yu, J., Wu, H., Sun, J. et al. (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Boil., 8, e1000533.
29. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
30. Saeed, A.I., Bhagabati, N.K., Braisted, J.C., Liang, W., Sharov, V., Howe, E.A., Li, J., Thiagarajan, M., White, J.A. and Quackenbush, J. (2006) TM4 microarray software suite. Methods Enzymol., 411, 134-193.
31. Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
32. Rosenbloom, K.R., Dreszer, T.R., Long, J.C., Malladi, V.S., Sloan, C.A., Raney, B.J., Cline, M.S., Karolchik, D., Barber, G.P., Clawson, H. et al. (2012) ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res., 40, D912-D917.
33. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
34. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
35. Curradi, M., Izzo, A., Badaracco, G. and Landsberger, N. (2002) Molecular mechanisms of gene silencing mediated by DNA methylation. Mol. Cell. Biol., 22, 3157-3173.
36. Koch, F., Jourquin, F., Ferrier, P. and Andrau, J.C. (2008) Genome-wide RNA polymerase II: not genes only! Trends Biochem. Sci., 33, 265-273.
37. Tatetsu, H., Ueno, S., Hata, H., Yamada, Y., Takeya, M., Mitsuya, H., Tenen, D.G. and Okuno, Y. (2007) Down-regulation of PU.1 by methylation of distal regulatory elements and the promoter is required for myeloma cell growth. Cancer Res., 67, 5328-5336.
38. Lai, A.Y., Fatemi, M., Dhasarathy, A., Malone, C., Sobol, S.E., Geigerman, C., Jaye, D.L., Mav, D., Shah, R., Li, L. et al. (2010) DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas. J. Exp. Med., 207, 1939-1950.
39. Jones, P.A. (1999) The DNA methylation paradox. Trends Genet., 15, 34-37.
40. Deaton, A.M. and Bird, A. (2011) CpG islands and the regulation of transcription. Genes Dev., 25, 1010-1022.