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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

Multi-dimensional perspective of chromosome 17 of the HCC2218 breast cancer cell line. Copy number, LOH, and DNA methylation, and profiling identifies an amplification of ERBB2 coinciding with allelic imbalance and loss of methylation. When examining the gene expression, the expression of HCC2218 is significantly higher than a panel of normal luminal and myoepithelial cell lines [29].
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Figure 8: Multi-dimensional perspective of chromosome 17 of the HCC2218 breast cancer cell line. Copy number, LOH, and DNA methylation, and profiling identifies an amplification of ERBB2 coinciding with allelic imbalance and loss of methylation. When examining the gene expression, the expression of HCC2218 is significantly higher than a panel of normal luminal and myoepithelial cell lines [29].

Mentions: Using the breast cancer cell line HCC2218, we show the integration of genomic, epigenomic, and transcriptomic data. Interestingly, when we examine the ERBB2 gene on chromosome 17, we show concurrent amplification, LOH, loss of methylation and drastic increase in gene expression (Figure 8). ERBB2 has shown to be an important gene in breast cancer development and therapeutic intervention. This demonstrates the value in integrating multiple dimensions to understand complex alteration patterns in disease samples where multiple causes can lead to a single effect.


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)

Multi-dimensional perspective of chromosome 17 of the HCC2218 breast cancer cell line. Copy number, LOH, and DNA methylation, and profiling identifies an amplification of ERBB2 coinciding with allelic imbalance and loss of methylation. When examining the gene expression, the expression of HCC2218 is significantly higher than a panel of normal luminal and myoepithelial cell lines [29].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Multi-dimensional perspective of chromosome 17 of the HCC2218 breast cancer cell line. Copy number, LOH, and DNA methylation, and profiling identifies an amplification of ERBB2 coinciding with allelic imbalance and loss of methylation. When examining the gene expression, the expression of HCC2218 is significantly higher than a panel of normal luminal and myoepithelial cell lines [29].
Mentions: Using the breast cancer cell line HCC2218, we show the integration of genomic, epigenomic, and transcriptomic data. Interestingly, when we examine the ERBB2 gene on chromosome 17, we show concurrent amplification, LOH, loss of methylation and drastic increase in gene expression (Figure 8). ERBB2 has shown to be an important gene in breast cancer development and therapeutic intervention. This demonstrates the value in integrating multiple dimensions to understand complex alteration patterns in disease samples where multiple causes can lead to a single effect.

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