Figure 1. Key for figures and hypothesis tables.

Green and red boxes = observed increases and decreases, respectively, in RNA expression of a given gene. Gene expression is depicted as “exp” followed by the National Center for Biotechnology Information gene symbol in parentheses. Yellow and blue boxes = biologic processes or protein activities that are inferred by the CNM approach to increase or decrease upon treatment, respectively. Darker shades of yellow or blue = stronger concordance. Numbers in the blue or yellow boxes indicate the number of gene expression state changes that support the inference: negative numbers indicate an inferred decrease and positive numbers indicate an inferred increase. Numbers in the green or red boxes indicate the log fold change.