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Open Access Highly Accessed Database

GCOD - GeneChip Oncology Database

Fenglong Liu1, Joseph A White2*, Corina Antonescu2, Daniel Gusenleitner2 and John Quackenbush2

Author Affiliations

1 Monsanto Company, 8520 University Green, Middleton, WI 53562, USA

2 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215, USA

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BMC Bioinformatics 2011, 12:46  doi:10.1186/1471-2105-12-46

Published: 3 February 2011

Abstract

Background

DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data.

Description

To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays.

Conclusion

The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface.