Figure 3.

Example model profiles overview interface. The example data is drawn from an experiment measuring the response of gastric epithelial cells infected with the vacA^-mutant strain of the pathogen Helicobacter pylori [3]. The data was sampled at five time points 0 h, .5 h, 3 h, 6 h, and 12 h. The data set was filtered to contain only the 2989 genes with no missing data (though STEM can handle missing data without filtering, see 1) that exhibited a .8 log base two fold increase or decrease for at least one time point. The number in the top left-hand corner of a profile box is the profile ID number. The colored profiles had a statistically significant number of genes assigned. Non-white profiles of the same color represent profiles grouped into a single cluster. By clicking on one of the buttons along the bottom of the window, a dialog window appears by which the profiles can be reordered by various criteria. Another button displays a table of all genes passing filter and the profile to which they were assigned. Clicking on a profile box brings up detailed information about the profile (Figure 5).