June 17, 2004 | DNA microarrays are now ubiquitous tools in biological laboratories. Although the explosion of microarray data raises concerns about the quality of information due to inconsistent experimental design, at the same time researchers are able to include additional controls and replicates that are key to the rigorous statistical analyses necessary to render data into knowledge.
Various commercial solutions exist to analyze microarray data, from enterprise-level solutions designed primarily for large companies and institute-based support facilities to the more recently emerged desktop solutions for individual research labs. One of the pioneers of the latter format is VizX Labs, founded in 2001 in Seattle by Bob Cottingham and Tom Ranken. VizX Labs' GeneSifter package aims to provide a straightforward, easy-to-navigate Web-based solution for microarray analyses that does not require an expert's understanding of statistical software. GeneSifter frees the user from having to update databases, make refinements to the software, and maintain backups, all of which is done behind the scenes at VizX Labs.
The product was released in 2002 and has been updated quarterly, most recently in April 2004. "It was apparent that something was needed to deliver the power of microarrays to individual researchers," Cottingham says. "So we provided an accessible product that integrates statistical analysis with the determination of biological significance."
 EASY AS PIE CHART: VizX Labs' GeneSifter is designed to help scientists analyze microarray data without requiring expertise in using statistical software. |
Microarray powerhouses such as Affymetrix and Agilent do provide enterprise-level tools, which generally include hardware, software, and customer-support applications. These solutions tend to be directed to informatics specialists at microarray centers within larger organizations, with price tags in the six-figure range. The limited supply of computational gurus often creates data-analysis bottlenecks in these centers. Moreover, control of data analysis is taken away from bench researchers.
"The situation reminded me of the days when people were dependent on large, centralized computer centers and arcane DOS-like interfaces," Cottingham says. "Desktop alternatives like Windows freed users to wield the power of computing themselves. Web-based GeneSifter gives scientists access in a venue they are already familiar with to a solution that not only provides lists of genes, but also helps them understand the biology."
The result is the development of simpler, cheaper desktop packages designed to walk the biologist through the process with an easy-to-navigate interface, while retaining the power of traditional approaches. Increasingly seen as complementing rather than competing with enterprise solutions, suppliers such as Affymetrix have become active supporters of third-party software developers such as VizX Labs. One advantage for the individual academic researcher is that the software tends to come with a much smaller price tag: in the $3,000-$10,000 range, which is accessible to most labs.
Products similar to GeneSifter can be found in roughly the same price range. Silicon Genetics' GeneSpring is comparable, although it is not a Web-based package. Another example is Iobion's GeneTraffic and ArrayAssist. A key factor is integration of data analysis with gene ontology databases. GeneSifter provides full integration, while other packages offer a standalone data-analysis package that can be combined with database-integration software at an additional cost. Iobion's ArrayAssist package can be combined with PathwayAssist for about $10,000.
Robert M. Frederickson is a biotech writer based in Seattle. He can be reached at rfreder@yahoo.com.