Topology of the Endomesoderm Network. The Endomesoderm GRN, as used in this analysis. Reproduced from  (version of December 2007) with permission from E.H. Davidson. Horizontal lines with bent outward arrow indicate genes. Arrows towards genes indicate activators of transcription, barred lines incident to genes indicate inhibitors of expression. Each gene is assumed to be exclusively regulated by the interactions shown. Protein interactions are indicated by circles. For details of the model, please refer to Additional Files 1 and 6. Genes or proteins without any input shown were set manually in simulations. Cis-regulatory inputs to genes that have not been identified by experimental analysis are denoted 'Ubiq', 'Mat' denotes amternal inputs, 'nucl.' indicates nuclearization and 'X' refers to the source of β-catenin. The different territories simulated contain the same set of possible interactions but due to temporally differing inputs, different subsets are realized in each territory.