Methods for the identification of a drug target, wherein the drug target is a component of a signal transduction pathway, are provided. The methods are based, in part, on selection of a gene of therapeutic interest and determination of regulatory DNA sequences which regulate expression of the gene in a cell of interest, followed by reconstruction of signal transduction pathways which act on molecules which bind to the regulatory sequence. Also provided are methods for assessing potential pharmacological effects and/or side effects of an agent, based on the effect of the agent on the distribution and properties of accessible regions in cellular chromatin.