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Overall, preservation of caudate nucleus modules was better in the frontal cortex (BA4) than in cerebellum.
However, the FC4neg3 module was slightly less preserved in cerebellum, compared to caudate nucleus; modules FC4pos3, FC4pos4 and FC4neg4 were slightly better preserved in cerebellum.
Only three out of 19 cortex modules, one out of 23 caudate nucleus modules and one out of 22 cerebellum modules show strong evidence of preservation.
When we analyzed the preservation of the caudate nucleus modules [ 27] in another HD dataset (HD-II) [ 35], we observed very high Z-summary scores for most modules, indicating a good reproducibility and thus robustness of the HD networks.
While the correlation of modules in the cerebellum and frontal cortex BA4 networks was largely comparable, the correlation of the caudate nucleus modules was higher, highlighting the prominent pathology in the striatum of HD patients (compare Figure 1B, D and F).
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The model deep cerebellar nucleus module also implements the inhibitory projection neuron (IDCN).
For example, 45% (p = 2.8 × 10-53) of genes overlapped between the yellow cortex module (labeled yellow/CTX) and yellow caudate nucleus module (labeled yellow/CN).
Additional file 4: Figure illustrating the remaining caudate nucleus network modules.
Next, we analyzed the preservation of the caudate nucleus network modules in gene expression datasets of other disorders.
In terms of cellular location, for example, Module One is enriched in the membrane and nucleus, whereas Module Two is enriched in the intracellular space.
The percentage of fluorescent VGAT or VGLUT1 puncta was automatically counted using the MetaMorph Count Nuclei application module (Molecular Devices).
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