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

doi:10.1186/1471-2105-9-422

BMC Bioinformatics
Volume 9

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Chari R
Coe BP
Wedseltoft C
Benetti M
Wilson IM
Vucic EA
MacAulay C
Ng RT
Lam WL

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Chari R
Coe BP
Wedseltoft C
Benetti M
Wilson IM
Vucic EA
MacAulay C
Ng RT
Lam WL
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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

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

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

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

author email corresponding author email

BMC Bioinformatics 2008, 9:422doi: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 SIGMA²as a novel tool to facilitate the high throughput systems biology analysis of cancer.