The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.
This invention was made with Government Support under Contract No. DE-FG02-04ER63803 awarded by the Department of Energy, Grant No. EF-0425719 awarded by the National Science Foundation and Grant No. HV28178 awarded by the National Institutes of Health. The Government has certain rights in this invention.