Ideker's team was able to identify new transcription factor binding patterns by borrowing a concept from computer science. The team considered the binding of one transcription factor to one gene as analogous to one "hop" of a data packet from one Internet router to another.
In the case of gene regulation, Ideker's team identified "2hop" relationships by first focusing on single transcription factor-gene associations, plus other experimental evidence that indicates that that gene regulates a second gene.
To enlarge the scope of the model further, Ideker's group also incorporated other previously discovered transcription-factor interactions and related genetic results. They relied on a total of eight types of direct and indirect evidence to create a model. That model predicts 980 as-yet-undiscovered transcription factor-gene binding interactions.
"This 'systems biology' approach, using so many different lines of evidence, has given us a much more revealing and detailed picture of how cells orchestrate gene regulation to cope with different environments," said Ideker. "We're far from understanding the full picture of gene regulation in a cell, but this new information should give scientists who are interested in blocking transcription factors a powerful new tool to narrow their search to the most promising candidates."