GeneGo adds tissue gene expression database to MetaCore

Applied Biosystems and GeneGo collaborate to integrate ABI\'s Tissue Gene Expression Database into the MetaCore data mining platform.

Jeffrey Bouley
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FOSTER CITY, Calif.—In a move to enhance the ability of researchers to study dif­ferential gene expression, life sciences company Applied Biosystems and GeneGo, a provider of software and databases for systems biol­ogy, have entered into a col­laboration under which GeneGo has integrated the Applied Biosystems Tissue Gene Expression Database into its MetaCore data min­ing platform. The integration of this proprietary data into MetaCore is expected to save researchers both time and costs that would otherwise be required to generate com­parable comprehensive and high-quality curated data.
"The whole idea is to give researchers good baseline data when looking at tis­sue samples," says Chris Grimley, product line direc­tor for Applied Biosystems. "By giving them this sort of data from the start, it makes their jobs much easier. Alternately, if you don't have this data already at hand, then you have to go through the process of generating it your­self, and that means extra time and extra money expended."
According to Applied Bio, the tissue expression database is a proprietary dataset of genome-wide gene expression values from 31 normal tissues and a "universal human reference RNA" which can serve as a baseline reference for microarray results and a source for identifying tissue-specific genes.
The combined Applied Bio-GeneGo solution is said to be particularly useful in facilitating microarray experiments, such as comparing gene expression chang­es in normal versus diseased or treated human tissues.
"Organ, tissue and cell type specificity are extremely impor­tant in human and other mam­malian gene expression analysis," says Tatiana Nikolskaya, CSO and founder of GeneGo. "The Applied Biosystems Tissue Expression Database is high-quality, standardized and very well annotated data. We have integrated it as a tissue expression filter in our latest product release to replace the publicly available, but less consistent, UniGene data, and look forward to collaborating on additional ways to leverage our complementary solutions."
Grimley agrees that there are potential opportunities for further collaboration, but declined to spec­ulate on what form such collabora­tions might take.
Although neither side is com­menting on the specific financial details of the deal, Grimley notes that MetaCore's popularity in the research community was a key reason for teaming with GeneGo. "Working with GeneGo allows us to reach their very wide install base, which includes a number of academic institutions," he says.
MetaCore is used by major pharmaceutical companies and numerous academic institutions for target selection and validation, identification of biomarkers for disease states and toxicology anal­ysis. According to GeneGo and Applied Bio, the integrated analy­ses afforded by using MetaCore helps accelerate the drug discov­ery and development process and also helps eliminate drug candi­dates that will have harmful side effects or interactions before they are tested in humans.
"GeneGo has a strong track record of integrating best-of-class technologies and data into its soft­ware platform to support emerg­ing systems biology applications," said Carl Hull, vice president for the sequence detection system and microarray business units of Applied Biosystems. "This collab­oration represents a mutually ben­eficial way to support our respec­tive customers in their endeavors to turn their valuable data into meaningful information in the drug discovery and development process."

Jeffrey Bouley

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