Fig. 4: Neuron clusters exhibited spatial co-expression patterns. | Nature Communications

Fig. 4: Neuron clusters exhibited spatial co-expression patterns.

From: Single-nucleus and spatial signatures of the brainstem in normal brain and mild traumatic brain injury in male mice

Fig. 4

a By performing hdWGCNA, we identified eight distinct expression patterns across the total neuron clusters. b kME map displaying the top 10 module genes and their connectivity within each pattern. c UMAP plot showing the clustering of gene expression patterns, with Model 1 being spatially close to Model 7, indicating similar expression patterns. d In addition to performing hdWGCNA, we also conducted hub gene scoring and found that neuronal clusters, such as noradrenergic, Serotonergic, and Dopaminergic neurons, Glu-GABA-Net-choline, and Net-Glu, which were located adjacent to each other, shared common patterns and up-regulated Models 3 and 5 (M3 and M5). High M3 scores were primarily observed around the fourth ventricle. KEGG analysis revealed that the hub genes were enriched in the GABAergic synapse and retrograde endocannabinoid signalling pathways. e Neuron clusters, such as Gly-Glu and Gly-Glu-GABA were located in the spinal trigeminal nucleus but were down-regulation genes in Model 2 (M2). Hub gene scoring also confirmed low scores in the spinal trigeminal nucleus (Sp5). f The widely distributed neuron cluster GABA (Reln)-Glu up-regulated genes in M1 and M7. These up-regulated hub genes were associated with cell contact and synapse interaction processes, as shown by GO and KEGG analyses. All the GO and KEGG analyses were conducted by hypergeometric test and BH multiple hypothesis-testing.

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