title: arrayMap 2014: an updated cancer genome resource.
abstract: Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64,000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China haoyang.cai@gmail.com.
authors.forename: Haoyang
authors.initials: H
authors.lastname: Cai
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland.
authors.forename: Saumya
authors.initials: S
authors.lastname: Gupta
authors.affiliation: Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Prisni
authors.initials: P
authors.lastname: Rath
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland.
authors.forename: Ni
authors.initials: N
authors.lastname: Ai
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland michael.baudis@imls.uzh.ch.
authors.forename: Michael
authors.initials: M
authors.lastname: Baudis
mesh_terms: D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis