Abstract A39: The UCSC Cancer Genomics Browser
Authors: Brian Craft, Kyle Ellrott, Mary Goldman, Christopher Wilks, Christopher Szeto, Singer Ma, Josh Stuart, Jingchun Zhu, David Haussler
Journal: Cancer Research (2011)

Abstract The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple datasets can be viewed simultaneously as coordinated “heatmap tracks” to compare across studies or different data modalities. Clinical information is encoded in color and shown as “clinical heatmap.” The browser provides interactive and dynamic views of the data from whole-genome scale to base-pair resolution, as well as interactive zooming onto a subset of the sample population. Users can order, filter, aggregate, classify, and display data interactively based on any given feature set including clinical features, annotated biological pathways, and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within each dataset. In June 2011, we deployed the current new site that supports a public portal, controlled-access portal for the TCGA consortium, Stand Up To Cancer breast cancer project, l-SPY clinical trial, and UCSF pancreas cancer project. User can view multiple project data, which she/he is authorized to access, under a single web page. In order to achieve this, we re-architected our system for a major data access security upgrade as well as deployed UCSC cancer browser user account. Although our public portal does not require an account to obtain access, user can control and store their favorite genesets, signatures, and manage their passwords if an account is established. An account and project-specific authorization are required for access to non-public tier data. Since the initial launch in November 2008, the cancer browser now contains large number of publicly accessible cancer genomic data, including 50 TCGA public-tier datasets and 19 other published studies (gene expression, copy number, DNA methylation, mutation and clinical information), corresponding to genome-wide experiments from 24488 samples across 15 cancers. Many new features have been added, including a tumor image viewer called hgMicroscope and a genomic signature evaluator, called hgSignature. User can define a genomic signature as any arithmetic formula calculated on a set of genes, such as a gene expression profile that correlates with better survival. User can also apply several gene expression signatures we derived from published studies on any browser track. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A39.