One of the major goals in biology is to reconstruct the complex genetic networks that operate inside cells, and to “film” how these networks evolve during the course of an organism’s development.
Today, Eric Xing and buddies at Carnegie Mellon University in Pittsburgh claim to have worked out how the way patterns of gene expression change in fruitflies over the course of their entire development. That’s a world first and no mean feat to boot.
Here’s how they did it. The new work relies on an impressive study from 2002 in which the activity of over 4000 fruitfly genes were measured at 66 points in its life cycle. Each of these snapshots produced a map of the gene network at that instant.
The question that Xing and co have answered is how these networks are related. That’s deceptively difficult because the networks are huge and significantly rewired between each snapshot.
But by assuming that the networks evolve into each other and so must share common features, the team were able to reverse-engineer what was going on using a machine learning algorithm called TESLA. The result is a kind of “movie” of gene network evolution during a fruitfly’s life.
Their conclusion is that 23 networks can describe the process of network evolution in fruit flies and that these networks appear to rewire themselves over time in response to the developmental requirement of the organism.
Until now most people have treated these kinds of networks as static entities rather than evolving ones. The new work opens up the possibility of studying the evolution of genetic networks in everything from cancer cells to immune response to development.
So plenty of back slapping all round at CMU.
Ref: arxiv.org/abs/0901.0138: Time-Varying Networks: Recovering Temporally Rewiring Genetic Networks During the Life Cycle of Drosophila melanogaster