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. 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 'omicsŐ. 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.