A user's guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Mary J. Goldman; Junjun Zhang; Nuno A. Fonseca; Isidro Cortés‐Ciriano; Qian Xiang; Brian Craft; Elena Piñeiro-Yáñez; Brian D. O’Connor; Wojciech Bażant; Elisabet Barrera; Alfonso Muñoz-Pomer Fuentes; Robert Petryszak; Anja Füllgrabe; Fátima Al‐Shahrour; Maria Keays; David H. Haussler; John N. Weinstein; Wolfgang K. Huber; Alfonso Valencia; Peter J. Park; Irene Papatheodorou; Jingchun Zhu; Vincent Ferretti; Miguél Vázquez

doi:10.1038/s41467-020-16785-6

BioinformaticsNature CommunicationsJul 7, 2020

Peer-reviewed journal article

A user's guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Mary J. Goldman iD, Junjun Zhang iD, Nuno A. Fonseca iD, Isidro Cortés‐Ciriano iD, Qian Xiang iD, Brian Craft iD, Elena Piñeiro-Yáñez iD, Brian D. O’Connor iD, Wojciech Bażant, Elisabet Barrera iD, Alfonso Muñoz-Pomer Fuentes iD, Robert Petryszak iD, Anja Füllgrabe iD, Fátima Al‐Shahrour iD, Maria Keays iD, David H. Haussler iD, John N. Weinstein iD, Wolfgang K. Huber iD, Alfonso Valencia iD, Peter J. Park iD, Irene Papatheodorou iD, Jingchun Zhu iD, Vincent Ferretti iD, Miguél Vázquez iD

Abstract

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project has generated, to our knowledge, the largest whole-genome cancer sequencing resource to date. Here we provide a users guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper: The ICGC Data Portal, UCSC Xena, Expression Atlas, PCAWG-Scout, and Chromothripsis Explorer. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, as well as demonstrate how the tools can be used together to more deeply understand tumor biology. Together, these tools enable researchers to dynamically query complex genomics data and integrate external information, enabling and enhancing PCAWG data interpretation. More information on these tools and their capabilities is available from The PCAWG Data Portals and Visualizations Page (http://docs.icgc.org/pcawg).

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