Fig. 1
Rescue conditions queried in the M-module framework. Gene expression profiles across the miR-138/SIN3A, NEDD8/SYVN1, and Temperature rescue conditions used to build differential gene co-expression networks. A binary co-expression network was constructed in which genes were selected based on the absolute value of Pearson correlation of the expression profiles of two genes. Only edges whose correlation exceeded a pre-defined threshold were included. Edges were then weighted (wi,j) based on the p values (pi and pj) of differential gene expression between the baseline and rescue conditions. Multiple differential co-expression networks were then analyzed to identify shared and unique multiple differential modules. 1-Modules are unique to a single rescue condition, whereas 2-Modules are found across two rescue conditions, and 3-Modules are found in all three rescue conditions. Adapted from [24]