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Genomic Networking (No, Not That Kind) Stirs on the Horizon

SAN DIEGO, June 6 - Networking has arrived in the lab, but it's not your father's back-slapping, business-card-trading variety.


Research conducted in recent months has finally armed scientists with the tools to analyze "broad concepts in details," said Terry Gaasterland, chair of the networks and metabolic pathways session of the conference and head of the laboratory of computational genomics at Rockefeller University.


This work has led to the publication of "some very large data sets, protein-protein interaction, and large genome data sets with replications," all of which has "put us over the top [for] analysis of gene expression and protein interactions [together] for true honest to goodness integrative analysis," she declared at the Beyond Genome conference held here.


Some of these broad concepts are regulatory-protein pathways and gene-regulation studies that add layers of complexity--and greater accuracy--to basic single protein-protein interactions.


Work presented at the meeting that help define these concepts include research conducted by Shoshana Wodak of the Université Libre de Bruxelles, who discussed her aMAZE database. This tool uses general rules for associating molecules and interactions into large complex networks like metabolic pathways, protein-protein interactions, and gene regulation.


Then there was Harvard Medical School's Sui Huang, who talked about genomic-regulatory networks. He used as an example the many ways in which aspirin influences a cell and how, by measuring those genetic subsystems, researchers will be able to zero in on the drug's side effects.

Additionally, Christopher Rao, at Lawrence Berkeley National Laboratory, discussed the emergence of comparative network analysis in his work exploring the bacterial chemotaxis of E. coli and B. subtilis.


"Biologists have very traditional ways of organizing information," explained Gaasterland. "What we're seeing in regulation of gene and protein expression is the chopping up of modules in different ways than the classical view. What's emerging is a different definition of pathway."


This emergence of ways to efficiently explore newly identified networks has piqued interest beyond academia.


"Drug companies don't want to pursue just proteins; they want to focus on pathways, so it's a valuable product," said Clarissa Desjardins, executive vice president for business development at Montreal-based Caprion Pharmaceuticals. Companies are "forced to move to systems biology," she said. "There's too much data to do it any other way."


The next steps network analysis must take to prove itself will include scaling up from five to 10 components to analyses with 200 or more parts. In addition, the field must move from studying microbial networks to those of humans and mice, said Gaasterland.

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