Figure 2.

A cavity map of the 60 highest differentially expressed pathways. The fold change scale for the pathways is shown using a log₂ scale (e.g., 6 on this scale is 64-fold change). The fold change is relative to nontuberculosis lung from control subjects, not normal-appearing tissue from subjects with tuberculosis. There is a functional “hole” in the cavity center, as can be seen by amount of pathways with blue color. However, not all pathways were downregulated in the cavity center; it can be seen that up to a quarter were actually upregulated. In contradistinction, the cavity wall had the most pathways upregulated and had the most intensely upregulated pathways of all. There are several prominent “nonimmunological” pathways that were among the top 60 expressed pathways, including, for example, colorectal cancer metastasis signaling via WNT signaling, and p38 MAPK signaling, downregulated in the cavity center but upregulated in the cavity wall.