Figure 3

Functional module analyses. (A) Bars represent the average percentage of overlap in COGs [37] categories within module predictions at different MCL inflation values [35] for the S. meliloti (Sm) network and the average values of 100 random networks created with the same number of nodes and interactions as the Sm dataset. Black arrow stands for the Inflation value chosen for further analyses. Error bars are negligible and not shown for clarity. The percentage of overlap for each module was obtained by considering only the most abundant COGs category in the module. (B) Functional overlap of modules related to membership of COGs functional categories. (C) Accuracy of the functional network to predict correct COGs (FC) and symbiosis-stage annotations (SS) [see Additional file 2] in functional modules using a leave-one-out cross-validation procedure. Bars indicate the frequency of correct COGs/symbiosis-stage assignments. Two measures of stringency were employed: high (HS) and low stringency (LS). RA and RS refers to random networks of equal size to the S. meliloti network generated for COGs and symbiosis-stage correct annotation comparisons, respectively. Error bars indicate standard deviation for 100 replicate random controls.