Interaction of the Most Upregulated and Downregulated Transcripts with the Actin Cytoskeleton. The conceptual network was predicted using the Cytoprophet module of Cytoscape [24-26], and therefore is solely based on information included on specialized interaction databases. Input transcripts included those from the top up- and down- regulated transcripts (Tables 2 and 3), and cDNAs taken from the previous interaction network (Figure 3). A significant probability of interaction (P-value > 0.9) is indicated as a thick edge. Node colors follow the same convention as in Figure 3, and hit count data can be found in Tables 2 and 3. This network includes 64 interactions (33 with P > 0.9) between 38 gene products. Genes without Cytoprophet-predicted interactions are not included, except for two interactions with Actin-P that were not predicted by Cytoprophet but that can be found in the literature (indicated with arrows). Interestingly, the previously featured network (Figure 3) connects the two groups of up- and downregulated transcripts in this figure. However, as Cytoprophet gathers experimental interaction data from specialized databases, some interactions depicted in Figure 3 are not shown (for example between POLB and ACTINP), because this data is not present on those source databases used by Cytoprophet for prediction.
Barrantes et al. BMC Genomics 2010 11:115 doi:10.1186/1471-2164-11-115