Table S1.
Functional gene groups showing significantly increased transcriptional coupling in pairs of connected brain regions (relative to unconnected pairs) are mainly related to neuronal connectivity and communication
| GO category | Description | No. of genes | P value |
| GO:0048167 | Regulation of synaptic plasticity | 84 | 0.0014 |
| GO:0007270 | Neuron–neuron synaptic transmission | 45 | 0.0039 |
| GO:0048168 | Regulation of neuronal synaptic plasticity | 37 | 0.0062 |
| GO:0045837 | Negative regulation of membrane potential | 7 | 0.0063 |
| GO:0035235 | Ionotropic glutamate receptor signaling pathway | 19 | 0.014 |
| GO:0060078 | Regulation of postsynaptic membrane potential | 35 | 0.018 |
| GO:0006414 | Translational elongation | 29 | 0.021 |
| GO:0050806 | Positive regulation of synaptic transmission | 63 | 0.023 |
| GO:0050808 | Synapse organization | 77 | 0.024 |
| GO:0008344 | Adult locomotory behavior | 66 | 0.026 |
| GO:0060079 | Regulation of excitatory postsynaptic membrane potential | 31 | 0.031 |
| GO:0097090 | Presynaptic membrane organization | 7 | 0.034 |
| GO:0051650 | Establishment of vesicle localization | 74 | 0.036 |
| GO:0035249 | Synaptic transmission, glutamatergic | 28 | 0.036 |
| GO:0050685 | Positive regulation of mRNA processing | 16 | 0.036 |
| GO:0051648 | Vesicle localization | 80 | 0.039 |
| GO:0045454 | Cell redox homeostasis | 46 | 0.04 |
| GO:0061001 | Regulation of dendritic spine morphogenesis | 16 | 0.04 |
| GO:0050770 | Regulation of axonogenesis | 77 | 0.041 |
| GO:1903313 | Positive regulation of mRNA metabolic process | 19 | 0.041 |
| GO:2000463 | Positive regulation of excitatory postsynaptic membrane potential | 12 | 0.041 |
| GO:0022900 | Electron transport chain | 32 | 0.042 |
| GO:0042775 | Mitochondrial ATP synthesis-coupled electron transport | 15 | 0.042 |
| GO:0051899 | Membrane depolarization | 67 | 0.043 |
| GO:0007628 | Adult walking behavior | 33 | 0.043 |
| GO:0007416 | Synapse assembly | 27 | 0.043 |
| GO:0022904 | Respiratory electron transport chain | 28 | 0.044 |
| GO:0006626 | Protein targeting to mitochondrion | 24 | 0.045 |
| GO:0021885 | Forebrain cell migration | 32 | 0.047 |
| GO:0007015 | Actin filament organization | 88 | 0.048 |
| GO:0097105 | Presynaptic membrane assembly | 5 | 0.049 |
GO biological process categories are listed in increasing order of their false discovery rate-corrected P values. Repeating the analysis including annotations for cellular components revealed similar categories related to neurites and synapses as well as the respiratory chain and oxidoreductase complex (Table S2).