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


CONCLUSIONS
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.
Chari
Raj
R
Department of Cancer Genetics and Developmental Biology, BC Cancer Agency Research Centre, Vancouver, BC, Canada. rchari@bccrc.ca
Coe
Bradley P
BP
Wedseltoft
Craig
C
Benetti
Marie
M
Wilson
Ian M
IM
Vucic
Emily A
EA
MacAulay
Calum
C
Ng
Raymond T
RT
Lam
Wan L
WL
D000465:Algorithms; D000818:Animals; D003196:Computer Graphics; D004273:DNA, Neoplasm / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D023281:Genomics / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
D004273:DNA, Neoplasm; D014157:Transcription Factors