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 . 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 Additional file 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).