Schematic of the approach. (A) Flowchart describing the steps to reconstruct our initial transcriptional regulatory network. (B) A set of gene expression profiles (matrix E) and about a proposed structure for the underlying transcriptional regulatory network (matrix S(0)) are used as inputs for Network Component Analysis (NCA). NCA uses an algorithm that first calculates the expected transcription factor activities (matrix A), and then recalculates S based on the new values of A, until both matrices converge. The outputs of this procedure are A* and S*, final values of A and S, which provide information about transcription factor activity as well as regulatory structure, respectively.