Marmal-aid--a database for Infinium HumanMethylation450.
Marmal-aid--a database for Infinium HumanMethylation450.
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DOI：
10.1186/1471-2105-14-359
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发表时间：
2013-12-12
影响因子：
3
通讯作者：
Rakyan VK
中科院分区：
文献类型：
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作者：
Lowe R;Rakyan VK
DNA甲基化对于人类基因组的正常功能是不可或缺的。目前，有越来越多的DNA甲基化组学数据在公共领域发布，允许有机会调查DNA甲基化组，基因组功能和人类表型之间的关系。Illumina450K是评估DNA甲基化的最受欢迎的平台之一，在公共领域有超过10，000个样本。然而，访问所有这些数据需要下载每个单独的实验，并且由于注释不一致，访问正确的数据可能是一个挑战。在这里，我们介绍“Marmal-aid”，第一个标准化的DNA甲基化数据库（可在www.example.com免费获得）。在Marmal-aid中，大多数公开可用的Illumina HumanMethylation 450数据被合并到一个单一的存储库中，允许重新处理数据，包括标准化和缺失值的插补。该数据库可通过两种方式访问：（1）使用R包以允许并入现有的分析管道，然后可以容易地查询该分析管道以深入了解某些CpG位点的功能。这是针对一个生物信息学家的经验，在R。(2)使用图形界面，允许普通生物学家查询预定义的一组组织（目前为15个），为Illumina HumanMethylation 450分析的450，000个CpG位点提供这些组织中甲基化状态的参考数据库。Marmal-aid是最大的公开可用的Illumina HumanMethylation 450甲基化数据库，将来自多个来源的Illumina HumanMethylation 450数据组合到具有单一通用注释格式的单个位置。这允许使用R包进行自动提取，并包含到现有的分析管道中。Marmal-aid还提供了一个易于使用的GUI，以可视化各种参考组织的用户定义的基因组区域中的甲基化数据。
DNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to investigate the relationships between the DNA methylome, genome function, and human phenotypes. The Illumina450K is one of the most popular platforms for assessing DNA methylation with over 10,000 samples available in the public domain. However, accessing all this data requires downloading each individual experiment and due to inconsistent annotation, accessing the right data can be a challenge. Here we introduce ‘Marmal-aid’, the first standardised database for DNA methylation (freely available at http://marmal-aid.org). In Marmal-aid, the majority of publicly available Illumina HumanMethylation450 data is incorporated into a single repository allowing for re-processing of data including normalisation and imputation of missing values. The database is accessible in two ways: (1) Using an R package to allow for incorporation into existing analysis pipelines which can then be easily queried to gain insight into the functionality of certain CpG sites. This is aimed at a bioinformatician with experience in R. (2) Using a graphical interface allowing general biologists to query a pre-defined set of tissues (currently 15) providing a reference database of the methylation state in these tissues for the 450,000 CpG sites profiled by the Illumina HumanMethylation450. Marmal-aid is the largest publicly available Illumina HumanMethylation450 methylation database combining Illumina HumanMethylation450 data from a number of sources into a single location with a single common annotation format. This allows for automated extraction using the R package and inclusion into existing analysis pipelines. Marmal-aid also provides a easy to use GUI to visualise methylation data in user defined genomic regions for various reference tissues.
影响因子：
64.5
作者：
Okano, M;Bell, DW;Li, E
通讯作者：
Li, E
影响因子：
3.7
作者：
Sandoval, Juan;Heyn, Holger A.;Esteller, Manel
通讯作者：
Esteller, Manel
DOI：
10.1038/nrg3000
发表时间：
2011-07-12
期刊：
Nature reviews. Genetics
影响因子：
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