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SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL - BMC Genomics (2006)

Bottom Line: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons.This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT

Background: The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.

Results: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.

Conclusion: In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.

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Related in: MedlinePlus

(A) Schematic of the basic architecture of SIGMA. Java WebStart technology was utilized to develop the main user interface to the database, ensuring users will be running the latest version of the program. The application is connected to the MySQL database through a JDBC driver provided by MySQL, over an Apache Web Server. (B) Outline of the various functionalities of SIGMA, with the five main types of visualization and analysis along with their associated uses.
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Figure 1: (A) Schematic of the basic architecture of SIGMA. Java WebStart technology was utilized to develop the main user interface to the database, ensuring users will be running the latest version of the program. The application is connected to the MySQL database through a JDBC driver provided by MySQL, over an Apache Web Server. (B) Outline of the various functionalities of SIGMA, with the five main types of visualization and analysis along with their associated uses.

Mentions: In order to increase the utility of this collection, a significant component of SIGMA is the web-based application which allows for the user-friendly mining of this dataset. Four major types of functionalities are offered by SIGMA: (1) interrogation of a single sample, (2) visualization and analysis of a single group of samples, (3) comparative analysis of two groups of samples, and (4) integration of data from multiple platforms (Figure 1B).


SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL - BMC Genomics (2006)

(A) Schematic of the basic architecture of SIGMA. Java WebStart technology was utilized to develop the main user interface to the database, ensuring users will be running the latest version of the program. The application is connected to the MySQL database through a JDBC driver provided by MySQL, over an Apache Web Server. (B) Outline of the various functionalities of SIGMA, with the five main types of visualization and analysis along with their associated uses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1764892&req=5

Figure 1: (A) Schematic of the basic architecture of SIGMA. Java WebStart technology was utilized to develop the main user interface to the database, ensuring users will be running the latest version of the program. The application is connected to the MySQL database through a JDBC driver provided by MySQL, over an Apache Web Server. (B) Outline of the various functionalities of SIGMA, with the five main types of visualization and analysis along with their associated uses.
Mentions: In order to increase the utility of this collection, a significant component of SIGMA is the web-based application which allows for the user-friendly mining of this dataset. Four major types of functionalities are offered by SIGMA: (1) interrogation of a single sample, (2) visualization and analysis of a single group of samples, (3) comparative analysis of two groups of samples, and (4) integration of data from multiple platforms (Figure 1B).

Bottom Line: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons.This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT

Background: The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.

Results: We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.

Conclusion: In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Show MeSH
Related in: MedlinePlus