Fig. 5

Concept Map view of iTerm:gene pairs. Genes from the input list with iTerms are in the vertical column at the center and iTerms are around the outside. The panel to the left is the legend explaining the graph, while the panel to the right allows manipulation of the output. This allows the user to switch the positions of the genes and iTerms, Search for specific genes or iTerms and to toggle the legend window on or off. The Load Expression File allows the user to load a file that indicates if a gene was up or down regulated in the experiment. Yellow corresponds to up while green to down regulated genes. The Save button allows the user to save either the graph text as a tab delimited two-column files or save the image. The Filter button allows the user to choose the minimum number of edges that a node must have to be visualized. See Fig. 6 for explanation of Subset Data