학술논문
A user guide for the online exploration and visualization of PCAWG data.
Document Type
article
Author
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; Valencia, Alfonso; Park, Peter J; Papatheodorou, Irene; Zhu, Jingchun; Ferretti, Vincent; Vazquez, Miguel
Source
Nature communications. 11(1)
Subject
Language
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.