Methylation plotter: A web tool for dynamic visualization of DNA methylation data

Source Code for Biology and Medicine

Volumn 9, Issue 1, 2014, Pages

  Mallona, Izaskun ^a,b   Díez Villanueva, Anna ^a,b   Peinado, Miguel A ^a,b  

^a Institute of Predictive and Personalized Medicine of Cancer (IMPPC)   (Spain)

^b Germans Trias i Pujol Health Research Institute   (Spain)

Author keywords

Lollipop plot; Methylation plot; Methylation visualization; R shiny

Indexed keywords

EID: 84903147184     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-9-11     Document Type: Review

References (15)

1. Esteller M. Cancer epigenomics: dna methylomes and histone-modification maps. Nat Rev Genet 2007, 8(4):286-298. 10.1038/nrg2005, 17339880.
2. Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007, 128(4):683-692. 10.1016/j.cell.2007.01.029, 3894624, 17320506.
3. Suzuki MM, Bird A. Dna methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008, 9(6):465-476. 10.1038/nrg2341, 18463664.
4. Peinado MA, . Jordà M Methods for dna methylation analysis and applications in colon cancer. Mutat Res Fund Mol Mech Mutagen 2010, 693(1):84-93. Jordà M.
5. Laird PW. Principles and challenges of genome-wide dna methylation analysis. Nat Rev Genet 2010, 11(3):191-203. 10.1038/nrg2732, 20125086.
6. Mesirov JP. Computer science. Accessible reproducible research. Science 2010, 327(5964):415-416. 10.1126/science.1179653, 3878063, 20093459.
7. Grunau C, Schattevoy R, Mache N, Rosenthal A. Methtools-a toolbox to visualize and analyze dna methylation data. Nucleic Acids Res 2000, 28(5):1053-1058. 10.1093/nar/28.5.1053, 102603, 10666443.
8. Xu Y, Manoharan HT, Pitot HC. Cpg analyzer, a windows-based utility program for investigation of dna methylation. Biotechniques 2005, 39(5):656. 10.2144/000112053, 16315371.
9. Xu Y-H, Manoharan HT, Pitot HC. Cpg patternfinder: a windows®-based utility program for easy and rapid identification of the cpg methylation status of dna. Biotechniques 2007, 43:334-342. 10.2144/000112537, 17907576.
10. Grunau C, Renault E, Rosenthal A, Roizes G. Methdb-a public database for dna methylation data. Nucleic Acids Res 2001, 29(1):270-274. 10.1093/nar/29.1.270, 29842, 11125109.
11. 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(21):4067-4068. 10.1093/bioinformatics/bti652, 16141249.
12. Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C. Biq analyzer ht: locus-specific analysis of dna methylation by high-throughput bisulfite sequencing. Nucleic Acids Res 2011, 39(suppl 2):551-556.
13. Kumaki Y, Oda M, Okano M. Quma: quantification tool for methylation analysis. Nucleic Acids Res 2008, 36(suppl 2):170-175.
14. RStudio I. Shiny: Web Application Framework for R. 2013, R package version 0.8.0. [http://CRAN.R-project.org/package=shiny].
15. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, Goldmann T, Seifart C, Jiang W, Barker DL, Chee MS, Floros J, Fan JB. High-throughput dna methylation profiling using universal bead arrays. Genome Res 2006, 16(3):383-393. 10.1101/gr.4410706, 1415217, 16449502.