Overview of the modules identification procedure. For each species, available co-expression, PPI, GI, and sequence data were extracted and converted into networks. For PPI and GI the networks representation is straightforward. For co-expression, sequence, and GO we computed a similarity score between genes and used a cutoff to construct a network. Expression, PPI, positive GI, and sequence were combined to create a joint weighted network where the weight is a function of the number of edges connecting two genes. Next, the MCL algorithm was applied on the combined network to identify modules for each species separately. See Methods and Supplementary Methods for details.
Zinman et al. BMC Systems Biology 2011 5:134 doi:10.1186/1752-0509-5-134