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Open Access Highly Accessed Methodology article

Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types

Noor B Dawany and Aydin Tozeren*

Author Affiliations

Center for Integrated Bioinformatics, Drexel University, Bossone Research Building 711, 3102 Market Street, Philadelphia, PA 19104, USA

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BMC Bioinformatics 2010, 11:483  doi:10.1186/1471-2105-11-483

Published: 27 September 2010

Abstract

Background

Much of the public access cancer microarray data is asymmetric, belonging to datasets containing no samples from normal tissue. Asymmetric data cannot be used in standard meta-analysis approaches (such as the inverse variance method) to obtain large sample sizes for statistical power enrichment. Noting that plenty of normal tissue microarray samples exist in studies not involving cancer, we investigated the viability and accuracy of an integrated microarray analysis approach based on significance analysis of microarrays (merged SAM) using a collection of data from separate diseased and normal samples.

Results

We focused on five solid cancer types (colon, kidney, liver, lung, and pancreas), where available microarray data allowed us to compare meta-analysis and integrated approaches. Our results from the merged SAM significantly overlapped gene lists from the validated inverse-variance method. Both meta-analysis and merged SAM approaches successfully captured the aberrances in the cell cycle that commonly occur in the different cancer types. However, the integrated SAM analysis replicated the known cancer literature (excluding microarray studies) with much more accuracy than the meta-analysis.

Conclusion

The merged SAM test is a powerful, robust approach for combining data from similar platforms and for analyzing asymmetric datasets, including those with only normal or only cancer samples that cannot be utilized by meta-analysis methods. The integrated SAM approach can also be used in comparing global gene expression between various subtypes of cancer arising from the same tissue.