BMC Bioinformatics Volume 9
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 SoftwareSIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomesRaj 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
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| 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. |