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. 2019 Dec 16;9(12):381. doi: 10.3390/brainsci9120381

Figure 1.

Figure 1

Cell Type Enrichment Results. We determined whether genes preferentially expressed in specific cell types were enriched in the genes differentially expressed between alcohol-dependent and control brain tissue using the userlistEnrichment function from the WGCNA package in R (see Methods). The human alcohol gene expression datasets are the rows (brain region of the dataset is shown in the first column) and the cell types are columns. Yellow indicates that the genes preferentially expressed in the cell type are up-regulated in alcohol-dependent brain tissue and blue indicates genes preferentially expressed in the cell type are down-regulated in alcohol-dependent brain tissue (Bonferroni-corrected p < 0.05). The p values associated with the enrichment are shown. If a cell type had more than one cell type marker gene list associated with it (from multiple publications, for example), the most significant p value is shown in the figure. See Table S2 for the full table of p values resulting from the enrichment analysis for all datasets. Some of the cell types were enriched in both the up-regulated and down-regulated datasets. The direction chosen for the figure was based on a more significant enrichment and greater number of enriched datasets for that cell type if applicable. These occurrences are denoted in the figure and described below. * Type I microglial genes were enriched in the down-regulated genes: purple_M4_Microglia(Type1)__CTX (p = 4.61 × 10−5) and pink_M10_Microglia(Type1)__HumanMeta (p = 6.43 × 10−5). ** magenta_M8_Microglia(Type2)_MouseMeta genes were enriched in the down-regulated genes (p = 3.11 × 10−7). + Astrocyte_probably__Cahoy genes were enriched in the up-regulated genes (p = 0.000178). ++ brown_M15_Astrocyte__CTX genes were enriched in the down-regulated genes (p = 0.00131). # Oligodendrocyte_probable__Cahoy genes were enriched in the down-regulated genes (p = 9.75 × 10−5). Note that Oligodendrocyte_definite__Cahoy genes were enriched in the up-regulated but not down-regulated genes for this dataset. BLA: basolateral amygdala, CNA: central nucleus of the amygdala, PFC: prefrontal cortex, NAC: nucleus accumbens, VTA: ventral tegmental area, HPC: hippocampus, Glut: glutamatergic.