SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data
SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data
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DOI：
10.1186/1471-2105-5-13
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发表时间：
2004-02-09
影响因子：
3
通讯作者：
Lam, WL
中科院分区：
文献类型：
--
作者：
Chi, B;deLeeuw, RJ;Lam, WL
背景：阵列比较基因组杂交（CGH）是一种检测DNA片段拷贝数差异的技术。人类基因组的完全测序和代表跨越整个人类基因组的数万个DNA片段的平铺集的阵列的开发使得整个基因组的高分辨率拷贝数分析成为可能。由于阵列CGH提供每个DNA片段的信号比，可视化将需要重新组装成染色体profiles.Results的个别数据点：我们已经开发了一个可视化工具，用于显示全基因组阵列CGH数据的背景下，染色体定位。SeeGH是一个应用程序，它将阵列CGH实验的点信号比数据转换为高分辨率染色体图谱的显示。从标准微阵列图像分析软件获得的简单制表符分隔的文本文件导入数据。SeeGH处理信号比数据，并以图形方式显示在传统的CGH核型图中，并增加了放大和DNA片段注释功能。在此过程中，SeeGH将数据导入数据库，计算每个重复点的平均比率和标准偏差，并将其链接到染色体区域以进行图形显示。一旦数据显示，用户可以选择隐藏或标记的DNA片段根据用户定义的标准，并检索注释信息，如克隆名称，NCBI序列登录号，比率，染色体上的碱基对位置，和标准deviation.Conclusions：SeeGH是一种新的软件工具，用于查看和分析阵列CGH数据。该软件使用户能够在整体基因组视图中查看数据，并放大特定的染色体区域，从而促进遗传变异的精确定位。SeeGH易于安装，并可在Microsoft Windows 2000或更高版本的环境中运行。
Background: Array comparative genomic hybridization ( CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles.Results: We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation.Conclusions: SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments.