Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows.

ABSTRACT: Improving the ability to reverse engineer biochemical networks is a major goal of systems biology. Lesions in signaling networks lead to alterations in gene expression, which in principle should allow network reconstruction. However, the information about the activity levels of signaling proteins conveyed in overall gene expression is limited by the complexity of gene expression dynamics and of regulatory network topology. Two observations provide the basis for overcoming this limitation: a. genes induced without de-novo protein synthesis (early genes) show a linear accumulation of product in the first hour after the change in the cell's state; b. The signaling components in the network largely function in the linear range of their stimulus-response curves. Therefore, unlike most genes or

SUBMITTER: Shimoni Y 

PROVIDER: S-EPMC2891706 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature