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SIGMA2 : A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes Chari, Raj; Coe, Bradley P.; Wedseltoft, Craig; Benetti, Marie; Wilson, Ian M.; Vucic, Emily A.; MacAulay, Calum; Ng, Raymond T.; Lam, Wan

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 SIGMA 2, 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 SIGMA 2 as a novel tool to facilitate the high throughput systems biology analysis of cancer.

Item Metadata

Title
SIGMA2 : A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
Creator
Chari, Raj; Coe, Bradley P.; Wedseltoft, Craig; Benetti, Marie; Wilson, Ian M.; Vucic, Emily A.; MacAulay, Calum; Ng, Raymond T.; Lam, Wan
Publisher
BioMed Central
Date Issued
2008-10-07
Description
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 SIGMA 2, 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 SIGMA 2 as a novel tool to facilitate the high throughput systems biology analysis of cancer.
Genre
Article
Type
Text
Language
eng
Date Available
2016-01-12
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0223324
URI
http://hdl.handle.net/2429/56455
Affiliation
Computer Science, Department of; Science, Faculty of
Citation
BMC Bioinformatics. 2008 Oct 07;9(1):422
Publisher DOI
10.1186/1471-2105-9-422
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
Chari et al.
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)