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A user guide for the online exploration and visualization of PCAWG data

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hdl:2117/328085

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Goldman, Mary J.
Zhang, Junjun
Fonseca, Nuno A.
Cortés-Ciriano, Isidro
Xiang, Qian
Craft, Brian
Piñeiro-Yáñez, Elena
O'connor, Brian D.
Bazant, Wojciech
Barrera, Elisabet
Muñoz-Pomer, Alfonso
Petryszak, Robert
Füllgrabe, Anja
Al-Shahrour, Fatima
Keays, Maria
Haussler, David
Weinstein, John N
Huber, Wolfgang
Park, Peter J.
Papatheodorou, Elena
Valencia, AlfonsoMés informació
Zhu, Jingchun
Ferretti, Vincent
Vazquez, Miguel
Document typeArticle
Defense date2020
PublisherSpringer Nature
Rights accessOpen Access
Attribution 3.0 Spain
Except where otherwise noted, content on this work is licensed under a Creative Commons license : Attribution 3.0 Spain
ProjectBARCELONA SUPERCOMPUTING CENTER - CENTRO. NACIONAL DE SUPERCOMPUTACION (MINECO-SEV-2015-0493)
Abstract
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.
Related documenthttps://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-16785-6/MediaObjects/41467_2020_16785_MOESM1_ESM.pdf
CitationGoldman, M.J. [et al.]. A user guide for the online exploration and visualization of PCAWG data. "Nature Communications", 2020, vol. 11, 3400. 
URIhttp://hdl.handle.net/2117/328085
DOI10.1038/s41467-020-16785-6
ISSN2041-1723
Publisher versionhttps://www.nature.com/articles/s41467-020-16785-6
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