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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D830-D835; doi:10.1093/nar/gkm802
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Nucleic Acids Research, 2008, Vol. 36, Database issue D830-D835
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

CanGEM: mining gene copy number changes in cancer

Ilari Scheinin1,2,3, Samuel Myllykangas3, Ioana Borze3, Tom Böhling3, Sakari Knuutila3 and Juha Saharinen1,2,*

1Genome Informatics Unit, Biomedicum Helsinki, Finland, 2Department of Molecular Medicine, National Public Health Institute of Finland, KTL and 3Departments of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland

* To whom correspondence should be addressed. Tel: +358 9 4744 8969; Fax: +358 9 4744 8480; Email: juha.saharinen{at}ktl.fi

Received August 15, 2007. Revised September 16, 2007. Accepted September 17, 2007.

The use of genome-wide and high-throughput screening methods on large sample sizes is a well-grounded approach when studying a process as complex and heterogeneous as tumorigenesis. Gene copy number changes are one of the main mechanisms causing cancerous alterations in gene expression and can be detected using array comparative genomic hybridization (aCGH). Microarrays are well suited for the integrative systems biology approach, but none of the existing microarray databases is focusing on copy number changes. We present here CanGEM (Cancer GEnome Mine), which is a public, web-based database for storing quantitative microarray data and relevant metadata about the measurements and samples. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. The CanGEM database can be accessed at http://www.cangem.org/.


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