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

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

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

Raj Chari,William W Lockwood,Bradley P Coe,Anna Chu,Devon Macey,Andrew Thomson,Jonathan J Davies,Calum MacAulay,Wan L Lam,

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.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes. Publishing Authors By Initials

R Chari,WW Lockwood,BP Coe,A Chu,D Macey,A Thomson,JJ Davies,C MacAulay,WL Lam,

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

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: BMC genomics

VOLUME: 7

Page Numbers: 324

Journal Abbreviation: BMC Genomics

ISSN: 1471-2164

DAY: 27

MONTH: 12

YEAR: 2006

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

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965258

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

KEYWORDS: Software

MESH TERMS: genetics

Chemical & Substance for Abstract: SIGMA: a system for integrative genomic microarray analysis of cancer genomes. Information

Substance Name: S100 calcium binding protein A10

Registry Number: 0

Grant and Affiliation Information for SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

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

Country: England

AGENCY: United States NIDCR

GRANT: R01 DE15965-01

ACRONYM: DE

MEDLINETA: BMC Genomics

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