arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

TL;DR

arrayMap is a comprehensive, curated database of over 40,000 high-resolution copy number alteration profiles across 224 human cancer types, enabling large-scale meta-analysis and systems-level oncogenomic research.

Contribution

It provides the first extensive, accessible resource for oncogenomic CNA data, integrating multiple datasets for broad cancer research applications.

Findings

Contains over 40,000 arrays from diverse cancer types

Facilitates gene-level and genome-wide data visualization

Supports meta-analysis and systems biology studies

Abstract

Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncoge- nomic array data. Methodology/Principal Findings: We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI's Gene Expression Omnibus (GEO), EBIs ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data re- view. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance: To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http://www.arraymap.org.