Workflow for the identification of transcriptional regulators for a specific gene.

The scheme shows the workflow of the different steps followed to identify potential transcriptional regulators for a given gene under LPS exposure. The upstream network was initially constructed using the PWMs from TRANSFAC® and the prediction algorithm MATCH™. The literature network downstream of LPS was inferred using the Pathway Studio knowledge database. These networks were merged and the merged network was contextualised using the booleanised genome-wide expression data. Finally, the ranking scheme with simple paths and essentiality metric resulted in a set of potential transcriptional regulators which were tested using siRNA mediated gene silencing experiments.