Empowering Biologists With Multi-Omics Data: Colorectal Cancer as a Paradigm

Bioinformatics. 2015 May 1;31(9):1436-43. doi: 10.1093/bioinformatics/btu834. Epub 2014 Dec 18.

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.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Colorectal Neoplasms / genetics*
  • Colorectal Neoplasms / metabolism
  • Epigenesis, Genetic
  • Gene Regulatory Networks
  • Gene Silencing
  • Genomics*
  • Humans
  • Neoplasms
  • Proteomics*
  • Software*
  • Transcriptome