Year-end Sale % OFF 
Abstract
Motivation: 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.Results: 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.Availability and implementation: The NetGestalt CRC portal can be freely accessed at http://www.netgestalt.org.Contact: bing.zhang@vanderbilt.eduSupplementary Information: Supplementary data are available at Bioinformatics online.
Highlights
Technology advancements have enabled comprehensive characterization of genomic, epigenomic, transcriptomic, proteomic and metabolomic changes in tumor specimens
Using colorectal cancer (CRC) as a paradigm, we describe the application of the NetGestalt framework to provide easy access and interpretation of multi-omics data
2.1.1 Sample types The portal includes data for both CRC tumors and cell lines. The former were collected from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), whereas the latter were from the Cancer Cell Line Encyclopedia (CCLE) project (Barretina et al, 2012) and the Achilles project (Cheung et al, 2011)
Summary
Technology advancements have enabled comprehensive characterization of genomic, epigenomic, transcriptomic, proteomic and metabolomic changes in tumor specimens. Using CircleMaps, the UCSC Interaction Browser allows simultaneous visualization of multiple omics datasets within the context of gene interactions (Wong et al, 2013). Very useful, this approach cannot scale up to large networks. Because it only uses one dimension to display network nodes, node-related information from different data sources can be rendered as ‘tracks’ along the vertical dimension for visual comparison and integration. This unique approach makes NetGestalt an appropriate framework for the study of multidimensional cancer omics data in the context of biological networks. We use three case studies to demonstrate that the portal provides for easy data querying and visualization and enables efficient data integration within a single omics data type, across multiple omics data types and over biological networks
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
