ExPlain identifies potential key regulatory molecules using a logical multi-step process (Fig. 1). First, promoters of differentially expressed genes are analyzed to identify specific combinations of transcription factors, referred to as composite modules, which regulate the expression of these genes. Then, the software analyzes signal transduction networks upstream of the composite modules to reveal specific key molecules that could potentially control the expression of these genes.

The potential key molecules can then be further validated by exploring the biological information provided in the BIOBASE Knowledge Library™ or by modeling the ExPlain-generated network(s) in Cell Illustrator™ in order to generate hypotheses for further experimental validation. Data quality is ensured through accurate full text manual curation of the scientific literature.