Shankar Ganesh, Rossi Michael R, McQuaid Devin E, Conroy Jeffrey M, Gaile Daniel G, Cowell John K, Nowak Norma J, Liang Ping
Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.
Cancer Inform. 2006;2:36-43.
Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/.
阵列比较基因组杂交（aCGH）是一种强大的高通量技术，用于检测癌症中的染色体拷贝数畸变（CNA），旨在从受影响的基因组区域中识别相关关键基因。然而，从包含数千行表格的数据集中筛选出少数候选基因可能是一个繁琐且耗时的过程。为了加快aCGH数据分析过程，我们开发了一个用户友好的aCGH数据查看器（aCGHViewer），作为aCGH数据表与基因组浏览器之间的桥梁。给定aCGH分析的数据显示在由单个染色体面板组成的基因组视图中，可以快速扫描这些面板以查找有趣的特征。可以选择包含感兴趣特征的染色体面板，以启动该单条染色体的详细窗口。在详细窗口中选择感兴趣的数据点会向UCSC或NCBI基因组浏览器发起查询，以便用户探索染色体区域中的基因内容。此外，aCGHViewer可以同时显示aCGH和表达阵列数据，以便直观地关联两者。aCGHViewer是一个独立的Java可视化应用程序，应与单独的统计程序结合使用。它可在所有主流计算机平台上运行，可从http://falcon.roswellpark.org/aCGHview/免费获取。
