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

Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL - BMC Bioinformatics (2008)

Bottom Line: However, software packages to handle, analyze, and visualize data from these multiple 'omics disciplines have not been adequately developed.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cancer Genetics and Developmental Biology, BC Cancer Agency Research Centre, Vancouver, BC, Canada. rchari@bccrc.ca

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.

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Related in: MedlinePlus

(A) Data hierarchy describing the relationship between platforms, assays and 'omics disciplines. (B) Functionality map of SIGMA2. List of the various functions and the output from that function that can be performed given the number of samples or sample groups and dimensions. Multiple sample analysis (single group and two group) are microarray platform independent. Functions listed in boxes are in addition to those listed in the box preceding the arrows.
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Figure 2: (A) Data hierarchy describing the relationship between platforms, assays and 'omics disciplines. (B) Functionality map of SIGMA2. List of the various functions and the output from that function that can be performed given the number of samples or sample groups and dimensions. Multiple sample analysis (single group and two group) are microarray platform independent. Functions listed in boxes are in addition to those listed in the box preceding the arrows.

Mentions: SIGMA2 is built to handle a variety of analysis techniques typically used in the high-throughput study of cancer, allowing the combinatorial integration of multiple 'omics disciplines. The hierarchy, which underlies the program, groups data into genome, epigenome, and transcriptome is shown in Figure 2A and the overall functionality map is given in Figure 2B and listed in Table 2. With each 'omics dimension, data sets may be imported representing any of the major types of biological measurements being assayed, for example, (i) examining both DNA copy number and LOH assays within the genomic bundle, (ii) examining both DNA methylation and histone modification status within the epigenomics bundle, and (iii) examining both gene expression profiles and microRNAs expression assays within the transcriptomic bundle. Each assay may branch into data sources from a multitude of technology platforms.


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

Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL - BMC Bioinformatics (2008)

(A) Data hierarchy describing the relationship between platforms, assays and 'omics disciplines. (B) Functionality map of SIGMA2. List of the various functions and the output from that function that can be performed given the number of samples or sample groups and dimensions. Multiple sample analysis (single group and two group) are microarray platform independent. Functions listed in boxes are in addition to those listed in the box preceding the arrows.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2571113&req=5

Figure 2: (A) Data hierarchy describing the relationship between platforms, assays and 'omics disciplines. (B) Functionality map of SIGMA2. List of the various functions and the output from that function that can be performed given the number of samples or sample groups and dimensions. Multiple sample analysis (single group and two group) are microarray platform independent. Functions listed in boxes are in addition to those listed in the box preceding the arrows.
Mentions: SIGMA2 is built to handle a variety of analysis techniques typically used in the high-throughput study of cancer, allowing the combinatorial integration of multiple 'omics disciplines. The hierarchy, which underlies the program, groups data into genome, epigenome, and transcriptome is shown in Figure 2A and the overall functionality map is given in Figure 2B and listed in Table 2. With each 'omics dimension, data sets may be imported representing any of the major types of biological measurements being assayed, for example, (i) examining both DNA copy number and LOH assays within the genomic bundle, (ii) examining both DNA methylation and histone modification status within the epigenomics bundle, and (iii) examining both gene expression profiles and microRNAs expression assays within the transcriptomic bundle. Each assay may branch into data sources from a multitude of technology platforms.

Bottom Line: However, software packages to handle, analyze, and visualize data from these multiple 'omics disciplines have not been adequately developed.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cancer Genetics and Developmental Biology, BC Cancer Agency Research Centre, Vancouver, BC, Canada. rchari@bccrc.ca

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.

Show MeSH
Related in: MedlinePlus