The new publicly available program, called GRAM (Genetic Regulatory Modules), incorporates two different data sets, each of which tells scientists something about gene regulatory pathways, to reveal the cell's internal wiring system. The first data set identifies molecules called regulators that bind to genes to switch them on, the second describes the levels of the products of these genes at any given time.
"Each data set independently really isn't sufficient to give us the exact causal relationship between the two," says MIT computer scientist David Gifford. "But here, with this program, we're bringing the cellular network into focus by having different perspectives of the network and then putting them together."
Typically, researchers take the "one witness" approach when trying to map regulatory pathways in cells: They examine only the levels of a gene product called messenger RNA -- the molecule that a gene produces to transport its encoded protein recipe to the cell's protein-production machinery. By measuring these levels, researchers hope they can reverse-engineer regulatory pathways and eventually identify the regulators that originally caused the genes to produce them.
According to Whitehead scientist Richard Young, this one-data-set approach is akin to studying only a subset of the information available at a crime scene in order to determine the criminal's original in
Contact: Kelli Whitlock or David Cameron
Whitehead Institute for Biomedical Research