Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data.
Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data.
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DOI：
10.1186/1471-2164-12-429
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发表时间：
2011-08-24
期刊：
影响因子：
4.4
通讯作者：
John SW
中科院分区：
文献类型：
--
作者：
Howell GR;Walton DO;King BL;Libby RT;John SW
我们介绍青光眼发现平台（GDP），一个在线环境，用于青光眼复杂转录分析数据集的轻松可视化和查询。我们还报告了Datgan的可用性，这是一套用于构建GDP的脚本。这个可重复使用的软件系统补充了现有的存储库，如NCBI GEO或EBI ArrayExpress，因为它允许构建可搜索的数据库，以最大限度地了解用户选择的转录分析数据集。Datgan脚本用于构建基础数据表和形成GDP的Web界面。GDP使用来自青光眼小鼠模型的数据填充。数据是使用DBA/2 J品系产生的，DBA/2 J品系是一种广泛使用的青光眼小鼠模型。DBA/2 J-Gpnmb+菌株提供了不发生青光眼的遗传匹配的对照菌株。我们分别评估了视网膜和视神经乳头，青光眼的重要组织。我们使用分层聚类来识别青光眼的早期分子阶段，这些阶段无法通过疾病的形态学评估来识别。GDP有两个组成部分。首先，交互式搜索和检索组件提供了在视网膜和视神经乳头两者中的疾病的所有鉴定阶段中评估感兴趣的基因的能力。输出以图形和表格格式返回，突出显示统计上的显著差异，以便于可视化分析。其次，批量下载组件允许差异表达基因的列表作为一系列与Excel兼容的文件被检索。为了便于获得感兴趣的基因的额外信息，GDP与选定的外部资源相关联，包括小鼠基因组信息学和在线Medelian人类遗传（OMIM）。Datgan构建的数据库允许用户友好地访问涉及疾病或发育阶段的时间顺序的数据集。Datgan和GDP可从http://glaucomadb.jax.org/glaucoma获得。
We introduce Glaucoma Discovery Platform (GDP), an online environment for facile visualization and interrogation of complex transcription profiling datasets for glaucoma. We also report the availability of Datgan, the suite of scripts that was developed to construct GDP. This reusable software system complements existing repositories such as NCBI GEO or EBI ArrayExpress as it allows the construction of searchable databases to maximize understanding of user-selected transcription profiling datasets. Datgan scripts were used to construct both the underlying data tables and the web interface that form GDP. GDP is populated using data from a mouse model of glaucoma. The data was generated using the DBA/2J strain, a widely used mouse model of glaucoma. The DBA/2J-Gpnmb+ strain provided a genetically matched control strain that does not develop glaucoma. We separately assessed both the retina and the optic nerve head, important tissues in glaucoma. We used hierarchical clustering to identify early molecular stages of glaucoma that could not be identified using morphological assessment of disease. GDP has two components. First, an interactive search and retrieve component provides the ability to assess gene(s) of interest in all identified stages of disease in both the retina and optic nerve head. The output is returned in graphical and tabular format with statistically significant differences highlighted for easy visual analysis. Second, a bulk download component allows lists of differentially expressed genes to be retrieved as a series of files compatible with Excel. To facilitate access to additional information available for genes of interest, GDP is linked to selected external resources including Mouse Genome Informatics and Online Medelian Inheritance in Man (OMIM). Datgan-constructed databases allow user-friendly access to datasets that involve temporally ordered stages of disease or developmental stages. Datgan and GDP are available from http://glaucomadb.jax.org/glaucoma.
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影响因子：
14.9
作者：
Blake JA;Bult CJ;Eppig JT;Kadin JA;Richardson JE;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
4.5
作者：
Libby RT;Li Y;Savinova OV;Barter J;Smith RS;Nickells RW;John SW
通讯作者：
John SW
影响因子：
4.4
作者：
Johnson, Elaine C.;Jia, Lijun;Morrison, John C.
通讯作者：
Morrison, John C.
DBA/2J小鼠的进行性神经节细胞丧失和视神经变性是可变且不对称的。
影响因子：
2.4
作者：
Schlamp, Cassandra L.;Li, Yan;Dietz, Joel A.;Janssen, Katherine T.;Nickells, Robert W.
通讯作者：
Nickells, Robert W.
视网膜神经节细胞变性是拓扑的，但在DBA/2J小鼠中不是特异性细胞类型。
影响因子：
7.8
作者：
Jakobs, Tatjana C;Libby, Richard T;Ben, Yixin;John, Simon W M;Masland, Richard H
通讯作者：
Masland, Richard H