Fig. 8

Eigengene network topology and connectivity differences within the Gupta dataset. a, b Eigengene networks as weighted graphs in a spring embedded layout for the Gupta Control (a) or ASD (b) groups. The spring-embedded layout places modules (nodes within the graphs) that are highly connected as much closer in space whereas modules that are less highly connected are repelled away from each other. The thickness of the connections (i.e., edges) between modules are scaled to connection strength whereby the thinnest line represents a correlation of r = −1 and the thickest line represents a correlation of r = 1. The color of each module node represents the ASD meta-module it belongs to. This was done to represent where the ASD meta-modules are located within the Control graph. The color-filled outlines around collections of modules represent the meta-module boundaries. Modules with a solid red or blue circle around it are modules that were identified in Figs. 1 and 2 as being replicably dysregulated in ASD across both datasets (blue = ASD-downregulated; red = ASD-upregulated). The dotted circles represent differentially expressed modules (FDR q < 0.05) present only within that specific dataset (see Additional file 4: Table S3). c Within (c) and outside (D) normative meta-module connectivity strength for each seed module depicted on the y-axis. The normative (Control-defined) meta-modules are denoted by the color of the rectangular outlines on the y-axis. Connectivity strength is depicted on the x-axis and for within meta-module connectivity is defined as the sum of connection strength between the seed module and all other modules within the seed module’s normative meta-module. Outside meta-module connectivity strength is defined as the sum of connection strength between the seed module and all other modules outside of the seed module’s normative meta-module. Turquoise bars indicated Controls and salmon-colored bars indicate ASD. The stars next to specific modules indicate a significant between-group difference in connectivity strength. d Eigengene networks as robust ME partial correlation matrices. Red coloring within the matrices indicates increasing positive correlation strength, while blue coloring indicates increasing negative correlation strength; see color bar for key indicating how color corresponds to correlation strength. Matrices have rows and columns ordered by hierarchical clustering based on the Control group, and the individual module numbers as well as meta-module colors are shown. Normative (Control-defined) meta-module boundaries are also clearly delineated by the black outlines over cells in the correlation matrices. Any cells with green outlines are those specific between-module connectivity comparisons that differed between-groups