The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.Database URL: http://dcc.icgc.org

A complex interplay of signaling events, including the Wnt pathway, regulates sprouting of blood vessels from preexisting vasculature during angiogenesis. Here we show that two distinct mutations in the (uro)chordate-specific Gumby/Fam105b gene cause an embryonic angiogenic phenotype in gumby mice. Gumby interacts with Disheveled 2 (Dvl2), is expressed in canonical Wnt-responsive endothelial cells and encodes an Ovarian Tumor Domain (OTU) class of deubiquitinase (DUB) that specifically cleaves linear ubiquitin linkages. A crystal structure of Gumby in complex with linear di-ubiquitin reveals how the identified mutations adversely impact substrate binding and catalytic function in line with the severity of their angiogenic phenotypes. Gumby interacts with HOIP/Rnf31, a key component of the linear ubiquitin assembly complex (LUBAC), decreases linear ubiquitination and activation of NFκB dependent transcription. This work provides support for the biological importance of linear (de)ubiquitination in angiogenesis, craniofacial and neural development and in modulating Wnt signaling.

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.Database URL: http://central.biomart.org.