coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.
coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.
复制标题
DOI：
10.1186/s12859-015-0568-2
复制
发表时间：
2015-04-28
影响因子：
3
通讯作者：
Bell JT
中科院分区：
文献类型：
--
作者：
Martin TC;Yet I;Tsai PC;Bell JT
表观基因组关联扫描是一种日益强大和广泛使用的方法，用于评估表观遗传变异在人类复杂性状中的作用。然而，这一迅速崛起的领域缺乏专门的可视化工具，无法显示表观遗传学数据集的特定特征。我们开发了Comet，这是一个R包和在线工具，用于可视化感兴趣的基因组区域中的Ewas结果。Comet生成表观遗传-表型关联结果和CpG位点之间估计的DNA甲基化相关性(共甲基化)的区域曲线图，并根据ENCODE数据、基因轨迹、参考CpG位点和用户定义的特征进一步选择可视化基因组注释。该工具可用于显示微阵列或基于测序的DNA甲基化数据的表型关联信号和相关模式，如Illumina Infinium450k、WGBS或MeDIP-Seq，以及其他类型的基因组数据，如基因表达谱。该软件是http://epigen.kcl.ac.uk/cometand提供的一个用户友好的在线工具，是R BioConductor的一个套装。GitHub上还提供了源代码、示例和完整文档。我们的新软件允许使用功能基因组注释和协甲基化模式的估计来可视化Ewas结果。Comet作为一个在线工具和R包可供广大受众使用，并可以成为解释快速增长的表观遗传学领域结果的宝贵资源。该软件是为表观遗传学数据设计的，但也可以应用于任何物种的基因组和功能基因组数据集。
Epigenome-wide association scans (EWAS) are an increasingly powerful and widely-used approach to assess the role of epigenetic variation in human complex traits. However, this rapidly emerging field lacks dedicated visualisation tools that can display features specific to epigenetic datasets. We developed coMET, an R package and online tool for visualisation of EWAS results in a genomic region of interest. coMET generates a regional plot of epigenetic-phenotype association results and the estimated DNA methylation correlation between CpG sites (co-methylation), with further options to visualise genomic annotations based on ENCODE data, gene tracks, reference CpG-sites, and user-defined features. The tool can be used to display phenotype association signals and correlation patterns of microarray or sequencing-based DNA methylation data, such as Illumina Infinium 450k, WGBS, or MeDIP-seq, as well as other types of genomic data, such as gene expression profiles. The software is available as a user-friendly online tool from http://epigen.kcl.ac.uk/cometand as an R Bioconductor package. Source code, examples, and full documentation are also available from GitHub. Our new software allows visualisation of EWAS results with functional genomic annotations and with estimation of co-methylation patterns. coMET is available to a wide audience as an online tool and R package, and can be a valuable resource to interpret results in the fast growing field of epigenetics. The software is designed for epigenetic data, but can also be applied to genomic and functional genomic datasets in any species.
登录
查看更多内容
影响因子：
48
作者：
Huber W;Carey VJ;Gentleman R;Anders S;Carlson M;Carvalho BS;Bravo HC;Davis S;Gatto L;Girke T;Gottardo R;Hahne F;Hansen KD;Irizarry RA;Lawrence M;Love MI;MacDonald J;Obenchain V;Oleś AK;Pagès H;Reyes A;Shannon P;Smyth GK;Tenenbaum D;Waldron L;Morgan M
通讯作者：
Morgan M
DOI：
10.1038/nrg3000
发表时间：
2011-07-12
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
9.8
作者：
Grundberg, Elin;Meduri, Eshwar;Deloukas, Panos
通讯作者：
Deloukas, Panos
DOI：
10.1093/bioinformatics/btq419
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Pruim RJ;Welch RP;Sanna S;Teslovich TM;Chines PS;Gliedt TP;Boehnke M;Abecasis GR;Willer CJ
通讯作者：
Willer CJ
影响因子：
46.9
作者：
通讯作者：
--