Figure 1

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.