Co-expressed genes tend to cluster into modules corresponding to major biological divisions (cell type, molecular function, etc.), as well as disease-relevant changes. Module summaries are presented for frontal cortex (top), neostriatum (middle), and white matter (bottom). The dendrograms group genes into distinct modules using hierarchical clustering. The y-axis corresponds to distance determined by the extent of topological overlap (1-TO). Top color band (Module label): dynamic tree cutting was used to identify highly parsimonious module definitions, generally dividing modules at significant branch points in the dendrogram. Second color band (CT vs. HIV): plotted T values of control vs. HIV + samples. Third color band (Encephalitis): plotted T values of HIV without encephalitis (groups B,C) vs. HIV with encephalitis (group D) samples. Fourth color band (Impairment): plotted correlations of GCR scores, our measure of neurocognitive impairment, across all HIV subjects. Fifth color band (CPE score): plotted correlations of CPE scores across all HIV subjects. Red corresponds to genes with higher expression in HIV, impairment score (GCR), HIVE, and CPE score for color bands two through five, respectively. Note that the most significant correlations with disease tend to occur in FC. Arrows within top color band indicates that these modules are enriched for genes showing increased or decreased expression in hippocampus of Alzheimer’s disease (Blalock et al. 2004; p < 0.00002).