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GeneGo Launches CF Tool


Cystic fibrosis-specific search and analysis options are available from MetaMiner CF.

By John Russell

April 1, 2008 | After just a few months of close collaboration with the Cystic Fibrosis Foundation Therapeutics (CFFT), GeneGo has launched MetaMiner CF, a disease-specific tool embedded in GeneGo's MetaCore pathway database and analysis platform. The new tool contains rich information about cystic fibrosis (CF) and represents "the first in a series of disease-centered MetaMiner projects," says Jule Bryant, GeneGo's VP of business development.

"CFFT approached GeneGo because we were looking for an informatics tool that would help integrate emerging data from biomarker and target identification projects with the known literature," says Diana Wetmore, VP of alliance management for CFFT, a non-profit drug discovery and development affiliate of the CF Foundation.

"What evolved was a collaborative effort. We recruited top CF academic and clinical researchers to work with the Gene-
Go developers. The researchers helped the developers and annotators comb through the literature to filter out dated and misleading information and focus on the... most relevant," Wetmore says.

The new tool, launched in February, is available at a discount to the roughly 4000 members of the CF Foundation. It's available at normal pricing to all researchers as part of GeneGo's MetaCore platform, said Bryant.

Because CF experts were involved, "[T]he information is current and based upon the latest understanding of disease mechanism," says Jerry Wright, a researcher at Johns Hopkins Medical Institutions Department of Physiology. "For instance, there has been a shift in the understanding of how TLR4 receptors in lung epithelium are involved in generating an inflammatory response to bacteria. Five or ten years from now, it would be generally accepted but would be difficult to pick out by a non-expert from current literature. This knowledge is reflected in the GeneGo map connections and the information on record justifying why this connection exists and why it disagrees with previously published studies."

CF is a disease that progresses over decades, affects multiple organ systems in a variable manner, and the end-stage bacterial infection has little or no direct connection to the underlying gene defect, says Wright. Presenting that in a 2-dimensional map environment is challenging. "The maps and networks will be periodically evaluated by CF experts and updated if necessary," he says.

Prioritizing Research
Wetmore suggests CF researchers might tackle several challenges with MetaMiner CF, including using the signaling networks to correlate proteomics data that might point to new therapeutic targets; using canonical maps to get quickly to the key literature; identifying new patterns of linked effects from complex microarray data; and creating visual displays of complex information that can be used as communication and collaboration tools.

"MetaMiner CF will have a dramatic impact on [the CF Foundation's] ability to visualize complex information and help prioritize research initiatives," she says.

CF researcher Raymond Frizzell, of the University of Pittsburgh School of Medicine, agrees the tools will help fill needed gaps. "The maps will help us be open to other possible interpretations for the data that we collect, by informing us that we are perturbing an entire system when we are testing a very specific hypothesis," he says. "Second, we will be able to approach the maps quantitatively and rank the significance of various pathways in affecting the CF related outcomes we study."

"Third, the CF field is always leading us into parts of the biological petri dish that we didn't anticipate, and the maps and the extended MetaCore structure will reduce or flatten the learning curve for moving into new areas. Fourth, it will permit young investigators who are entering the field to access and understand it more quickly, and for someone like me, the daunting area of infection/immunity can be better understood and perhaps even approached experimentally." 

 

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 This article appeared in Bio-IT World Magazine.
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