Version 1.2.0 added several new interface options to STEM. Some of these are illustrated below.

The new interface options can be accessed by pressing the new Interface Options button along the bottom of the interface.

The interface options window that appears when pressing the Interface Options button on the main interface. The new options allow all gene expression profiles assigned to a profile to be displayed on the main interface (Display all) and also just the subset that belong to a selected GO category or gene set (Display only selected). Also new in this version of STEM, the y-axis scale on profile detail windows, these are the windows which appear when pressing on a profile box, can be fixed to user defined parameters instead of being determined automatically by STEM. Also the x-axis can now be visualized with the time points placed proportional to the real sampling rate instead of being uniformly spaced.

Above illustrates the new option in STEM to display all the genes assigned to each profile as above. In the above image each gene assigned to the same profile are on the same y-axis scale, however the y-axis scales for different profiles are different. Scales can also be gene specific (shown below) or global where the scale is the same for all profiles.

A similar image to above, but each gene expression profile is scaled separately making the correspondence in shape with the model profile clearer.

The above image illustrates the new option to only display the selected genes when ordering profiles. The selected genes are those genes of the GO category or gene set for which the ordering is based. In this case only the expression profiles of the cell cycle annotated genes are plotted.

The x-axis of the profiles on the main interface with the time points placed proportional to the real sampling rate.

A profile details window with the x-axis proportional to the real sampling rate instead of uniformly spaced.