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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

Main structural components of SIGMA2. Data and genome mapping information is stored in the MySQL database. Segmentation analysis using DNACopy and GLAD and statistical analysis is performed using R, with results stored in database. Java was used to program the application, specifically for the user interface and the different types of visualization. Base-pair positions and gene annotations are linked to other biological databases to facilitate further interrogation by the user.
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Figure 1: Main structural components of SIGMA2. Data and genome mapping information is stored in the MySQL database. Segmentation analysis using DNACopy and GLAD and statistical analysis is performed using R, with results stored in database. Java was used to program the application, specifically for the user interface and the different types of visualization. Base-pair positions and gene annotations are linked to other biological databases to facilitate further interrogation by the user.

Mentions: SIGMA2 is implemented in Java, and requires version 1.6+ of the runtime compiler. In addition, the statistical package R and database application MySQL are also required. The java interface communicates with MySQL using a JDBC connector and with R using the JRI package by JGR (Figure 1). MySQL is used for data storage and querying while R is used for the segmentation and statistical analysis. All genomic coordinate information was obtained from University of California Santa Cruz (UCSC) genome databases [18].


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)

Main structural components of SIGMA2. Data and genome mapping information is stored in the MySQL database. Segmentation analysis using DNACopy and GLAD and statistical analysis is performed using R, with results stored in database. Java was used to program the application, specifically for the user interface and the different types of visualization. Base-pair positions and gene annotations are linked to other biological databases to facilitate further interrogation by the user.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Main structural components of SIGMA2. Data and genome mapping information is stored in the MySQL database. Segmentation analysis using DNACopy and GLAD and statistical analysis is performed using R, with results stored in database. Java was used to program the application, specifically for the user interface and the different types of visualization. Base-pair positions and gene annotations are linked to other biological databases to facilitate further interrogation by the user.
Mentions: SIGMA2 is implemented in Java, and requires version 1.6+ of the runtime compiler. In addition, the statistical package R and database application MySQL are also required. The java interface communicates with MySQL using a JDBC connector and with R using the JRI package by JGR (Figure 1). MySQL is used for data storage and querying while R is used for the segmentation and statistical analysis. All genomic coordinate information was obtained from University of California Santa Cruz (UCSC) genome databases [18].

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