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SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes

Raj Chari1*, Bradley P Coe1, Craig Wedseltoft1, Marie Benetti1, Ian M Wilson1, Emily A Vucic1, Calum MacAulay2, Raymond T Ng3 and Wan L Lam1

Author Affiliations

1 Department of Cancer Genetics and Developmental Biology, BC Cancer Agency Research Centre, Vancouver, BC, Canada

2 Department of Cancer Imaging, BC Cancer Agency Research Centre, Vancouver, BC, Canada

3 Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

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BMC Bioinformatics 2008, 9:422  doi:10.1186/1471-2105-9-422

Published: 7 October 2008

Abstract

Background

High throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packages to handle, analyze, and visualize data from these multiple 'omics disciplines have not been adequately developed.

Results

Here, we present SIGMA2, a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. Multi-dimensional datasets can be simultaneously visualized and analyzed with respect to each dimension, allowing combinatorial integration of the different assays belonging to the different 'omics.

Conclusion

The identification of genes altered at multiple levels such as copy number, loss of heterozygosity (LOH), DNA methylation and the detection of consequential changes in gene expression can be concertedly performed, establishing SIGMA2 as a novel tool to facilitate the high throughput systems biology analysis of cancer.