Fig. 9: Enrichment of cell-type marker genes in cycling mRNA modules. | Communications Biology

Fig. 9: Enrichment of cell-type marker genes in cycling mRNA modules.

From: Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus

Fig. 9

a Cell type clusters (n = 387) are collapsed into previously defined neighborhoods (MGE, DR/SUB/CA, CGE, L2/3 IT, L4/5/6 IT Car 3, NP/CT/L6b, PT, and Other). The “Other” neighborhood clusters were collapsed into their respective subclasses (Meis2, Oligo, CR, Astro, SMC-Peri, Micro-PVM, Endo, and VLMC). RAIN cycling mRNA modules enriched in cell-type marker genes and their respective cell-type subclasses are shown (PBH < 0.05). The size of datapoints represents the mean number of genes that are both a cell subclass marker gene and in a module, i.e., mean intersection size. Datapoints are colored by the mean −log10(PPH) of a cell type subclass’s marker genes enrichment in a cycling module. b Pathways enriched in the cortical grey60 module (Pg:SCS < 0.05; 10 ≤ term size ≤ 500). c mRNAs with an adjacency ≥0.03 are visualized (n = 180 of 290). mRNAs (circle nodes) are arranged based on co-expression adjacency (grey edges). Nodes of cycling genes are colored by period category. If a gene is not cycling, its node is colored grey. The hub gene has a diamond node. Genes that underwent immunohistochemistry analysis, Trf and Il33, have their nodes outlined in black and labels bolded.

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