Methylation plotter: a web tool for dynamic visualization of DNA methylation data
Tóm tắt
Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at
http://gattaca.imppc.org:3838/methylation_plotter/
.
Tài liệu tham khảo
Esteller M:Cancer epigenomics: dna methylomes and histone-modification maps. Nat Rev Genet. 2007, 8 (4): 286-298. 10.1038/nrg2005.
Jones PA, Baylin SB:The epigenomics of cancer. Cell. 2007, 128 (4): 683-692. 10.1016/j.cell.2007.01.029.
Suzuki MM, Bird A:Dna methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008, 9 (6): 465-476. 10.1038/nrg2341.
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.
Laird PW:Principles and challenges of genome-wide dna methylation analysis. Nat Rev Genet. 2010, 11 (3): 191-203. 10.1038/nrg2732.
Mesirov JP:Computer science. Accessible reproducible research. Science. 2010, 327 (5964): 415-416. 10.1126/science.1179653.
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.
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.
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.
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.
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.
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.
Kumaki Y, Oda M, Okano M:Quma: quantification tool for methylation analysis. Nucleic Acids Res. 2008, 36 (suppl 2): 170-175.
RStudio Inc.:Shiny: Web Application Framework for R. 2013, R package version 0.8.0. [http://CRAN.R-project.org/package=shiny].
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.