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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

Algorithm for integrating between different array platforms. Data for every platform is matched to genomic position. Subsequently, an interval-based approach is used to systematically query data for each interval. In this figure, the interval, k, is 10 kb in size. By converting everything to genomic position, samples sets of the same disease type but on different array platforms can be aggregated affording the user with additional statistical power.
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Figure 3: Algorithm for integrating between different array platforms. Data for every platform is matched to genomic position. Subsequently, an interval-based approach is used to systematically query data for each interval. In this figure, the interval, k, is 10 kb in size. By converting everything to genomic position, samples sets of the same disease type but on different array platforms can be aggregated affording the user with additional statistical power.

Mentions: SIGMA2 treats all data in the context of genome position based on the relevant human genome build using the UCSC genome assemblies. An interval-based approach is used to sample across different array platforms and assays and data from each interval are merged together. Briefly, this is done by querying data at fixed genomic intervals for each platform and subsequently taking an average of the measurements within each interval. The algorithm is listed in Figure 3.


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)

Algorithm for integrating between different array platforms. Data for every platform is matched to genomic position. Subsequently, an interval-based approach is used to systematically query data for each interval. In this figure, the interval, k, is 10 kb in size. By converting everything to genomic position, samples sets of the same disease type but on different array platforms can be aggregated affording the user with additional statistical power.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Algorithm for integrating between different array platforms. Data for every platform is matched to genomic position. Subsequently, an interval-based approach is used to systematically query data for each interval. In this figure, the interval, k, is 10 kb in size. By converting everything to genomic position, samples sets of the same disease type but on different array platforms can be aggregated affording the user with additional statistical power.
Mentions: SIGMA2 treats all data in the context of genome position based on the relevant human genome build using the UCSC genome assemblies. An interval-based approach is used to sample across different array platforms and assays and data from each interval are merged together. Briefly, this is done by querying data at fixed genomic intervals for each platform and subsequently taking an average of the measurements within each interval. The algorithm is listed in Figure 3.

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