Fang Hong, Harris Stephen C, Su Zhenjiang, Chen Minjun, Qian Feng, Shi Leming, Perkins Roger, Tong Weida
Z-Tech Corporation, An ICF International Company, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Division of Systems Toxicology, National Center for Toxicological Research (NCTR), FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Methods Mol Biol. 2017;1613:333-353. doi: 10.1007/978-1-4939-7027-8_13.
A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarrays, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data and the availability of functional information for data interpretation. At the FDA's National Center for Toxicological Research (NCTR), we are developing a public microarray data management and analysis software, called ArrayTrack that is also used in the routine review of genomic data submitted to the FDA. ArrayTrack stores a full range of information related to DNA microarrays and clinical and nonclinical studies as well as the digested data derived from proteomics and metabonomics experiments. In addition, ArrayTrack provides a rich collection of functional information about genes, proteins, and pathways drawn from various public biological databases for facilitating data interpretation. Many data analysis and visualization tools are available with ArrayTrack for individual platform data analysis, multiple omics data integration and integrated analysis of omics data with study data. Importantly, gene expression data, functional information, and analysis methods are fully integrated so that the data analysis and interpretation process is simplified and enhanced. Using ArrayTrack, users can select an analysis method from the ArrayTrack tool box, apply the method to selected microarray data and the analysis results can be directly linked to individual gene, pathway, and Gene Ontology analysis. ArrayTrack is publicly available online ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm ), and the prospective user can also request a local installation version by contacting the authors.
强大的生物信息学能力被广泛认为是实现毒理基因组学前景的核心。毒理基因组学方法（如DNA微阵列）的成功应用，与适当的数据管理、从海量数据中提取知识的能力以及用于数据解释的功能信息的可用性紧密相关。在美国食品药品监督管理局（FDA）的国家毒理学研究中心（NCTR），我们正在开发一款名为ArrayTrack的公共微阵列数据管理和分析软件，该软件也用于对提交给FDA的基因组数据进行常规审查。ArrayTrack存储了与DNA微阵列以及临床和非临床研究相关的全方位信息，以及源自蛋白质组学和代谢组学实验的经过整理的数据。此外，ArrayTrack还提供了从各种公共生物数据库中提取的关于基因、蛋白质和通路的丰富功能信息，以促进数据解释。ArrayTrack提供了许多数据分析和可视化工具，用于单个平台数据分析、多组学数据整合以及组学数据与研究数据的综合分析。重要的是，基因表达数据、功能信息和分析方法完全整合在一起，从而简化和增强了数据分析和解释过程。使用ArrayTrack，用户可以从ArrayTrack工具箱中选择一种分析方法，将该方法应用于选定的微阵列数据，分析结果可以直接链接到单个基因、通路和基因本体分析。ArrayTrack可在网上公开获取（http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm），潜在用户也可以通过联系作者请求获得本地安装版本。
