System for Integrative Genomic Microarray Analysis (SIGMA)

Category Genomics>Genetic Data Analysis/Tools and Cross-Omics>Knowledge Bases/Databases/Tools

Abstract System for Integrative Genomic Microarray Analysis (SIGMA) is a software application consisting of two (2) main components.

First, the database which contains genomic copy number profiles from over 175 commonly used cancer cell lines from multiple array Comparative Genomic Hybridization (CGH) platforms including the Affymetrix 10K, 100K and 500K arrays, the BCCRC SMRT array and the Stanford cDNA microarray.

Second, a web-based java application which is designed to provide easy and interactive online viewing of high resolution array CGH data.

Unlike other array databases which provide access to only raw data files or simplified views of the data, SIGMA aims to provide an interactive interface which is both user friendly and allows for advanced analysis of public array CGH data.

In addition to interfacing with over 100 cell lines profiled on the sub- mega-base resolution array CGH, this site will serve as a public repository for array CGH data generated from future publications in the manufacturer’s laboratory.

With a minimum of 10,000 data points per genome and over 175 cell line genomes characterized, this represents one of the most detailed array CGH databases currently available.

Users will find data present for many commonly used cancer cell lines derived from numerous tissue types including breast, lung, cervix, blood, prostate, and many others.

In the current version of SIGMA, users can interrogate single genomic profiles and perform comparisons across and between different groups of samples.

In addition, users can view samples profiled on multiple platforms to gain a better understanding of the various array CGH platforms.

As a prelude to future versions of the software, the manufacturer has included two cell lines which were also profiled with the MeDIP array CGH measuring whole genome methylation levels.

Subsequent version of this software will aim to integrate differential DNA methylation, loss of heterozygosity (LOH) and gene expression, in addition to the genome copy number data which exists.

Main functionalities of SIGMA -- Four (4) 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.

Visualization and interrogation of a single genome -- The first function is the ability to view a single high resolution array CGH profile at multiple magnification levels.

The major utility of this function is to display the underlying genomic architecture of a cell line, so that genetic features can be considered in experimental interpretation.

Using the interval search option, users can retrieve the genes which are located in a desired region and have the option to query commonly used biological databases such as National Center for Biotechnology Information (NCBI) OMIM, NCBI Gene, NCBI PubMed and the UCSC Genome Browser (see G6G Abstract Number 20197).

The utility of this function is to facilitate a direct connection from experimental findings to known, relevant information.

Moreover, the ability to interrogate for specific genes and regions can be done for any of the types of analysis/functionality outlined above.

Multiple genome comparison and mining across tumor types -- A common research question is to look across a series of samples with common phenotype to identify recurrent genetic changes.

With the spectrum of samples warehoused in SIGMA, such a query can be performed across multiple cancer types.

And, recurrent alterations detected in one group of samples can be compared against those in another group.

Simultaneous visualization of data from multiple platforms -- This SIGMA feature allows users to view multiple platforms of data simultaneously.

And it fulfills the need for cross platform comparison which is essential for the multi-dimensional descriptions of a genome.

Integrative visualization of DNA copy number and methylation -- One of the novel features the manufacturer has provided is the integrative visualization of copy number alterations with DNA methylation status.

The major premise in studying copy number alterations at the DNA level is that these are the primary changes involved in driving changes in gene expression.

Though gene dosage variation may be responsible for expression changes, alteration in DNA methylation pattern also contributes significantly to regulating gene expression.

Recently, methods for global methylation analysis to measure aberrant DNA methylation status across tumor genomes have been developed.

With increased prevalence of studies of whole genome methylation, this feature will be of greater importance.

Note: SIGMA's architecture facilitates the direct mining of genomic and epigenomic data, this can be easily adapted, and Not limited to, high resolution genetic and gene expression surveys.

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Manufacturer Web Site SIGMA

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G6G Abstract Number 20320

G6G Manufacturer Number 100443