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


CONCLUSIONS
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.
Chari
Raj
R
Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver, BC, Canada. rchari@bccrc.ca
Lockwood
William W
WW
Coe
Bradley P
BP
Chu
Anna
A
Macey
Devon
D
Thomson
Andrew
A
Davies
Jonathan J
JJ
MacAulay
Calum
C
Lam
Wan L
WL
D000230:Adenocarcinoma / Q000235:genetics; D017306:Annexin A2 / Q000235:genetics; D045744:Cell Line, Tumor / Q000378:metabolism; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics*; D016208:Databases, Factual; D018628:Gene Dosage; D018773:Genes, erbB-1; D016259:Genes, myc; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009418:S100 Proteins / Q000235:genetics; D012984:Software; D000099248:S100 Calcium Binding Protein A10
D017306:Annexin A2; D004273:DNA, Neoplasm; D009418:S100 Proteins; D000099248:S100 Calcium Binding Protein A10