Fig. 4

Identifying modules in a network. The jActiveModules plugin in Cytoscape 3.1.0 was also used to identify high-scoring differentially expressed (DE) sub-networks in the network of Fig. 3a (using parameter values: overlap threshold = 0.3; search depth = 2). The highest-scoring module identified in the network using a the gene expression data at 36 h post-infection (hpi) and b at 48 hpi, are shown. The InnateDB pathway analysis tool was used to identify over-represented pathways for c the 36 hpi module and d the 48 hpi module. Note that for this dataset, the top five pathways for the 36 and 48 hpi modules are very similar, which reflects a similar pattern of gene expression at these time-points in this dataset