VISIONET implementation uniqueness. (A) Comparison of VISIONET features with popular biological network visualisation analysis tools. VISIONET implements five features to facilitate expertise-driven visualisation and analysis of overlapping transcription factor networks. Using empirical evaluation based on our case study, the availability of these features was assessed in the most popular existing tools: CellDesigner v4.4 , PAYAO , Cytoscape v2.8 , VisANT 4.0 , and WikiPathways . (B) Schematic flowchart illustrating the architecture of VISIONET, designed to facilitate expertise-driven biological discovery. Gene expression and TF binding site data are supplied to VISIONET, and biologist interacts with VISIONET to determine which network components to display. Internally, VISIONET performs the computationally intensive task of data integration, graph layout and network filtering.