Zhu Jing, Shi Zhiao, Wang Jing, Zhang Bing
Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.
Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, USA.
Bioinformatics. 2015 May 1;31(9):1436-43. doi: 10.1093/bioinformatics/btu834. Epub 2014 Dec 18.
Recent completion of the global proteomic characterization of The Cancer Genome Atlas (TCGA) colorectal cancer (CRC) cohort resulted in the first tumor dataset with complete molecular measurements at DNA, RNA and protein levels. Using CRC as a paradigm, we describe the application of the NetGestalt framework to provide easy access and interpretation of multi-omics data.
The NetGestalt CRC portal includes genomic, epigenomic, transcriptomic, proteomic and clinical data for the TCGA CRC cohort, data from other CRC tumor cohorts and cell lines, and existing knowledge on pathways and networks, giving a total of more than 17 million data points. The portal provides features for data query, upload, visualization and integration. These features can be flexibly combined to serve various needs of the users, maximizing the synergy among omics data, human visualization and quantitative analysis. Using three case studies, we demonstrate that the portal not only provides user-friendly data query and visualization but also enables efficient data integration within a single omics data type, across multiple omics data types, and over biological networks.
The NetGestalt CRC portal can be freely accessed at http://www.netgestalt.org.
Supplementary data are available at Bioinformatics online.
近期完成的癌症基因组图谱（TCGA）结直肠癌（CRC）队列的全球蛋白质组学特征分析，产生了首个在DNA、RNA和蛋白质水平具有完整分子测量值的肿瘤数据集。以CRC为例，我们描述了NetGestalt框架的应用，以提供对多组学数据的便捷访问和解读。
NetGestalt CRC门户包括TCGA CRC队列的基因组、表观基因组、转录组、蛋白质组和临床数据，来自其他CRC肿瘤队列和细胞系的数据，以及关于通路和网络的现有知识，总共超过1700万个数据点。该门户提供数据查询、上传、可视化和整合功能。这些功能可以灵活组合以满足用户的各种需求，最大限度地发挥组学数据、人类可视化和定量分析之间的协同作用。通过三个案例研究，我们证明该门户不仅提供用户友好的数据查询和可视化，还能在单一组学数据类型内、跨多种组学数据类型以及在生物网络上实现高效的数据整合。
可通过http://www.netgestalt.org免费访问NetGestalt CRC门户。
补充数据可在《生物信息学》在线获取。
