After confirmation of the expression of certain genes in two different dengue-infected cell lines and in dengue patients, we Table S1 . Colour intensity is derived from mean relative expression fold changes of dye swap results in comparison to universal reference (Strategene USA), red for upregulated, green for down regulated, black for no change, and grey for missing data. Time course (3, 6, 12, 24, 48, selected those that were upregulated in at least one time point in HepG2 cells and in at least one time point in A549 cells and in dengue patient samples (comparing acute to convalescent blood samples). Fifty genes fulfilled these criteria (Table S2 ) and, we felt, represented common genes involved in dengue virus response, or virus replication, while excluding responses that were cell type specific. These 50 common genes were mapped by direct interactions using the MetaCore program which illustrated the close clustering and interconnectedness of a network of 29 of genes around NF-kB, TNF-a and STAT1. (Figure 3A) . The NF-kB gene alone was added to the network, despite not being from our common list, to illustrate the connections between those induced by it. For example, the upregulation of IP-10, I-TAC, VEGF, PAI1, B2M, TNFAIP3 and RIG-1 could all be linked to the activation of NF-kB, while NFKB1B and NFKB1A, two feedback control genes for NF-kB activation, were also upregulated reflecting the self containment of this activation ( Figure 3A ). The degree of upregulation varied between the genes in this pathway with I-TAC and IP-10 being the most highly up-regulated (average expression in the two cell types and patients) genes ( Figure 3B) . A number of genes clustered around STAT1 were associated with the IFN pathway, and examination of the common list revealed another four genes (viperin, IFI44, IFIH1, G1P3) related to the IFN pathway that were upregulated but not mapped by the MetaCore program ( Figure 3C ). Finally, a number of genes related to the ubiquitin-proteasome pathway also appeared on the MetaCore map (HERC5, USP18 and Hdm2) with several more (unmapped) genes appearing on the common list ( Figure 3D )