GenMAPP 2: new features and resources for pathway analysis
GenMAPP 2: new features and resources for pathway analysis
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DOI：
10.1186/1471-2105-8-217
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发表时间：
2007-06-24
影响因子：
3
通讯作者：
Pico, Alexander R.
中科院分区：
文献类型：
--
作者：
Salomonis, Nathan;Hanspers, Kristina;Pico, Alexander R.
背景：微阵列技术发展迅速，使生物学家能够量化各种物种的基因组范围内的基因表达水平、选择性剪接和序列变异。分析和显示这些数据提出了重大挑战。事实证明，基于通路的微阵列数据分析方法对于呈现数据和生成可检验的假设非常有用。结果：为了满足微阵列社区不断增长的需求，我们发布了基因图谱注释器和通路分析器 (GenMAPP) 的第 2 版，这是一个新的 GenMAPP 数据库模式，以及用于通路分析的集成资源。我们重新设计了 GenMAPP 数据库，以支持多个基因注释和物种，以及为可能无限数量的物种创建自定义物种数据库。我们利用同源信息来翻译物种之间的通路内容，并利用来自保守蛋白质相互作用和共表达的数据扩展现有通路，从而扩展了我们的通路资源。我们实现了一种新的数据可视化模式来支持复杂数据的分析，包括时间进程、单核苷酸多态性 (SNP) 和剪接。 GenMAPP 版本 2 还提供了创新的方法来显示和共享数据，通过将整组路径的分析的 HTML 导出合并为有组织的网页。结论：GenMAPP 版本 2 提供了一种快速查询复杂实验数据以了解多种生物体中路径水平变化的方法。
Background: Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses.Results: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages.Conclusion: GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.