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PAG Presenter Touts Web-Based Tool As Possible First Stop for Systems Genetics Analyses

By Andrea Anderson

SAN DIEGO (GenomeWeb News) – At the annual Plant and Annual Genomes meeting here yesterday, University of Tennessee neurogenetics researcher Robert Williams presented information on an open source web tool for doing systems analyses for a wide range of plant and animal species.

Williams described GeneNetwork as a collection of "tools that you can actually use" — a suite of resources for doing intended systems analyses, mapping, and data display combined with a database for genomic datam phenotype information, and more.

"A lot of you have generated the resources needed," Williams told PAG attendees during the plenary session. But, he noted, bringing together reams of genetic data with information on phenotype and other biological features on multiple scales can be tricky.

In an effort to simplify some early stages of this process, he and his colleagues at the University have been building the infrastructure for getting preliminary analyses — what he called "Mom and Pop analysis" — done quickly.

The software available currently allows for a range of relatively straightforward strategies for scrutinizing systems data. For example, GeneNetwork allows for principal component analysis using WebQTL, quantitative trait locus analyses and mapping, transcriptome mapping, network-level analyses, and so on.

The service is expected to expand as additional software is developed for solving increasingly complex analytic tasks, Williams said, noting that GeneNetwork developers are interested in collaborating with individuals working on codes for those more complex problems.

"We're focusing on the simple stuff," he said. "There are lots of opportunities to extend this, obviously."

GeneNetwork is already being used to bring together different streams of data generated on mice, humans, Drosophila, and other organisms, Williams explained. He suggested that researchers interested in setting GeneNetwork up to suit their own favorite plant or animal should contact developers to get the latest version of source codes.

Along with his pitch for the burgeoning analysis platform, Williams also emphasized the importance of finding ways to do high-throughput phenotyping for organisms of interest at multiple scales and establishing appropriate reference panels and populations to support systems genetics research.

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