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Agilent Tech Bets New Array-Analysis Software Will Woo Systems Biologists

Agilent Technologies this week launched GeneSpring GX 10.0, the next generation of its gene-expression bioinformatics platform. GeneSpring GX 10 offers tools for systems-level data interpretation and pathway analysis and was designed with systems biologists in mind, company officials said.
According to Agilent, the new product can enable users to analyze data from gene-expression, microRNA-expression, alternative-splicing, and RT-PCR experiments. The upgrade is part of an industry-wide trend that seeks to arm scientists with multiple applications to help them answer increasingly complex biological questions more effectively.
“The concept of systems biology has been around for over a decade, but the theory is now being put into practice at a rapid and accelerating pace,” Pam Tangvoranuntakul, Agilent’s GeneSpring product manager, told BioArray News this week.
“It’s critical that the field of bioinformatics provides scientists with tools that can be used to find linkages and concordance between the different data types so that biological knowledge can be extracted from this global data,” she said. “The major driver in developing GX 10 was to support the systems biological field in this endeavor.”
Like its predecessor, GeneSpring GX 9.0, GX 10 is the product of a collaboration between Agilent and Bangalore, India-based Strand Life Sciences. Strand had previously been assisting Stratagene develop multiple software packages to analyze array data, and Agilent continued the partnership after it bought Stratagene last year (see BAN 6/12/2007).
With Strand’s assistance, Agilent released GX 9.0 in February. Version 9.0’s visualization and analysis system for gene-expression data was built on Strand’s Avadis platform and included guided workflows for Agilent SurePrint microarrays, Affymetrix GeneChips, and Illumina Beadchips, said Tangvoranuntakul. GX 9.0 also could be used to highlight enriched pathways or gene ontology categories and offered users import networks and pathways from sources such as KEGG, the Cancer Cell Map, and BioCyc (see BAN 2/19/2008).
According to Tangvoranuntakul, due to its expanded features, “GeneSpring GX 10 is a much larger step than GX 9.0.” In addition to gene expression, the platform “now supports miRNA data, alternative splicing, RT-PCR, and pathway analysis,” she said. “Virtually any platform can be used with GeneSpring 10, even those that are not formally supported. Data from any microarray or RT-PCR platform can be imported and analyzed as custom data in GX 10,” said Tangvoranuntakul.
New Features
Tangvoranuntakul said that GeneSpring GX 10.0 has been designed to address the needs of customers who previously performed pathway analysis using separate software tools. “A critical part of gaining biological insight from statistical results is to determine how key molecules interact in a molecular network,” she said. “Currently, this network [or] pathway analysis is often performed in a separate analysis application from the one used to identify these key molecules.”

“The concept of systems biology has been around for over a decade, but the theory is now being put into practice at a rapid and accelerating pace.”

GX 10 can also correlate data between different array platforms, different organisms, and different data types. “GeneSpring GX allows you to translate data between mouse and human,” Tanvoranuntakul said, “finding corresponding genes in each organism so that you can quickly determine whether the genes that are differentially expressed in the mouse model are the same genes that are differentially expressed in the human experiment.”
Additionally, she said that GeneSpring GX 10.0 can work with different data types. “For example, you can identify differentially expressed microRNA, find their gene targets, and translate that list into the corresponding gene expression experiment to determine the gene expression levels of those predicted miRNA targets,” she said. “As more researchers adopt systems biology approaches, we’re giving them the ability to easily locate corresponding probes on different platforms or applications.”
Strand and Stratagene
Agilent and Strand first announced their intent to work together on GeneSpring in August 2007, building upon the prior agreement between Stratagene and Strand.
Strand and Stratagene originally joined forced in December 2005. Stratagene eventually offered its PathwayArchitect tool for pathway analysis and its ArrayAssist Expression and Exon software for expression analysis, both on the Avadis platform.
This week, Tangvoranuntakul said that Strand’s Avadis platform holds a “central role” in Agilent’s GeneSpring program, and could be seen as an associated benefit of the firm’s Stratagene acquisition. After signing last year’s agreement with Agilent, Strand Life Sciences CEO Vijay Chandru called Agilent an “ideal partner for us as we build out applications for systems biology and, more broadly, in drug discovery."
While the new versions of GeneSpring are the manifestations of the impact of the Stratagene buy on Agilent’s bioinformatics offering, the company has also been busy using Stratagene’s reagent-manufacturing capabilities to bolster its array platform.
In July, Yvonne Linney, Agilent’s general manager of genomics, told BioArray News that by the end of this year, all of the firm’s labeling kits will be manufactured by Stratagene. Linney said at the time that the firm is also looking to pair Stratagene’s portfolio of RT-PCR kits with its arrays for data validation, and plans to leverage Stratagene’s manufacturing capabilities in Agilent’s budding oligo library synthesis business (see BAN 7/8/2008).
The integration of Stratagene’s resources with Agilent’s array offering comes at a time when Agilent is rolling out its next-generation microarray platform. In June, the company launched the latest version of its DNA Microarray Scanner, capable of 2-micron-level resolution (see BAN 6/10/2008). By the end of this year, the firm also plans to have 1-million-feature arrays on the market.
The Competition
Agilent’s bioinformatics approach appears to differ from that employed by array rival Affymetrix, in that it has looked to build its bioinformatics resources internally and through acquisitions and partnerships. By comparison, Affymetrix has relied partially on its “GeneChip-compatible” program, the company recommends packages offered by external developers for use with its array platform.
Affy established the GeneChip-compatible program in 2005 (see BAN 10/7/2005). It has since deemed dozens of packages to be compatible and promotes software tools from 11 different developers, including SAS, Genedata, and Partek, for use in gene-expression analysis alone, among other companies and applications.
This week, Affy supplemented its current bioinformatics offering with a deal to distribute Biotique’s XRAY gene expression-analysis software directly to its customers (see Briefs, this issue). Agilent officials, however, were unable to comment on whether the firm envisions taking a similar approach to making third-party bioinformatics tools available for use with its chips in the future. 

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