Genencor International is assembling a group of leading bioinformaticists and gene regulation experts to form the EcoReg Consortium, a group charged with constructing and maintaining a database on the regulatory systems of Escherichia coli.
Founding members of the consortium include Peter Karp of SRI International; Milton Saier of the University of California, San Diego; Tyrrell Conway of the University of Oklahoma; and Adam Arkin of the University of California, Berkeley.
Currently, over 12 experts in the E. coli research field have agreed to participate as curators.
Genencor has put up the initial funding for the database, which will be freely available for both academic and commercial users at http://gobi.lbl.gov/~ecoreg. The project will encompass both database curation and the development of software tools for querying, scientific visualization, data-mining and modeling.
Michael Arbige, senior vice president of research and development for Genencor, said that the company would use its new transcriptional profiling technology as well as other new tools to derive information on the regulatory systems of E. coli. Transcriptional profiling tracks how every gene in a population behaves at any time and under varying conditions, such as under severe temperatures or pH.
EcoReg will complement the existing EcoCyc database of E. coli metabolic pathways built by Peter Karp and others. Karp said that EcoReg will serve as a repository for low-level functional genomic data sets for E. coli, while EcoCyc contains carefully curated information.
EcoCyc now contains descriptions of 550 E. coli transcription units, representing approximately 25 percent of the organism’s genes, Karp said.
Genencor will benefit from having a “first look” at the data that is posted on EcoReg as well as the tools that are developed through the efforts of the consortium.
Arbige sees the collaboratory approach of EcoReg as the best way to determine the regulatory pathways of E. coli.
“E. coli has between 4000 and 4500 genes and they’re all moving together at the same time under various sets of conditions. That’s a lot of data to interpret and we think that pulling the best of the best together will really move this information base forward.”
Arbige said that the database should be fully operational by May or June.