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Biobase Marks One-Year Anniversary of Proteome Acquisition with First Integrated Software Product

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Nearly a year to the day after acquiring Incyte's Proteome database unit, Biobase this week launched ExPlain, a pathway analysis software package that represents the first offspring of the firm's newly integrated development team.

ExPlain is also Biobase's first standalone software product. The company, known primarily for its BRENDA, Transfac, and Transpath databases, has integrated analytical tools with its database offerings in the past, but did not market any software until now. "To some extent, it's something new for us," Edgar Wingender, president and CSO, told BioInform. In addition to developing the software, he said, "we also had to develop the mechanism for developing the software."

In addition to its core team of developers in Wolfenbuttel, Germany, and the former Proteome group in Beverly, Mass., the company relied on a small team of software developers based in Novosibirsk, Russia, who worked on a contract basis to put the finishing touches on the product, Wingender said.

The market for pathway informatics tools is growing increasingly competitive, with players like Ingenuity, GeneGo, Ariadne, Stratagene, and others launching new tools that promise to map experimental data onto known pathways. Wingender said that ExPlain differs from other pathway software in the market, however, in its ability to offer "upstream" analysis of the promoter regions that ultimately govern gene expression.


"It was not found in the gene expression analysis or profiling. But from the promoter model that we developed, we could predict that this gene should play a role in a certain disease context, … and [a lab] verified with conventional methodology that this gene actually also was induced."

ExPlain draws from the information in Biobase's databases to perform a "systematic promoter analysis" for a given set of experimental data and build a model that includes the transcription factor binding site as well as the transcription factors and promoters involved in the pathway. "Once you're at that stage, you can go back to what you might call traditional pathway analysis," Wingender said, to determine "which pathway keeps these factors that you predict to be active in these promoters under control."

Wingender said that Biobase has validated the software in collaboration with several undisclosed German universities. As an example, he cited a case in which ExPlain was able to identify a target gene that was not on the microarray. "It was not found in the gene expression analysis or profiling. But from the promoter model that we developed, we could predict that this gene should play a role in a certain disease context," he said. "We predicted that, gave that knowledge back to the lab, and they verified with conventional methodology that this gene actually also was induced."

Biobase did not disclose pricing information for ExPlain.

Holger Karas, senior vice president of business development at Biobase, said that the product "relies on the whole set of databases coming from both the former Proteome and Biobase, and integrates all these databases into one tool, facilitating the pathway knowledge from Transpath, the transcription knowledge from Transfac, and particularly the very detailed disease annotation from the Proteome databases."

Karas said that the launch of the software is "practically the first result" of a year-long cross-Atlantic integration process following the acquisition, although he acknowledged that this kind of integration is "never really complete."

Wingender said that the "first step" in the integration process is "nearly completed," and involves streamlining the user interface between the two product lines so that Transfac and Transpath content are accessible via the Proteome products, and vice versa.

The "internal integration," which involves linking the products at a lower level, "may take a bit longer," he said.

Proteome was not profitable when Biobase acquired it last year, but Karas said that the company has been able to move the business into the black. Biobase is privately held, and has been break-even since 2003. The firm now employs around 60 people across its two locations, and has more than 550 academic customers and 50 commercial customers.

But even as the company wraps up its integration of the Proteome business, another integration project is around the corner. Karas said that the company has just signed an agreement with the University of Cardiff in Wales to distribute its Human Genome Mutation Database.

The HGMD was previously available as part of the Celera Discovery System, but that agreement expired last June.

Wingender said that integrating the HGMD data with its pathway databases will allow researchers to generate hypotheses about the role of particular mutations within biological pathways and networks, and ultimately enable them to predict the correlation between mutations and disease phenotypes.

HGMD is only the first of several new academic databases that Biobase has its eye on. "We're already looking for more databases because there are so many interesting resources in academia that would make sense to be commercialized," Karas said.

Wingender added that the company has "a list of ideas" for new database products, and is in discussions with several public domain database providers regarding licensing agreements.

The company is also expanding its operations to prepare for the new data. Karas said that Biobase is opening a facility in Bangalore, India, to supplement its development activities in Germany and Massachusetts. The Bangalore office will employ around 30 people, he said — around the same headcount as each of the firm's other two offices — and is expected to open some time in the fall.

Karas stressed that the Bangalore facility is not a sign that Biobase intends to reduce headcount in its other locations, however. "We're doing this to expand," he said. "We would never give away our experts."

— Bernadette Toner ([email protected])

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