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Fig. 4 | Biology Direct

Fig. 4

From: Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics

Fig. 4

RHY modifies the mouse brain transcriptome

(A) Volcano plots showing gene expression changes between RHY and saline conditions in female (F) and male (M) mice at ZT4 or ZT14. Green (female) and purple (males) datapoints indicate differentially expressed genes (DEGs; FDR < 0.05) between RHY100 and saline. Note that RHY changes gene expression in both directions. Black datapoints indicate transcripts without significant change.

(B) Heatmap of the Log2 fold change in expression of the DEGs found for ZT4F, ZT4M, ZT14F, and ZT14M. The 1324 DEGs found in at least one of the four comparisons are shown. Automated hierarchical clustering showing seven DEG clusters (C1-C7) is also represented.

(C) Zoom of cluster C1 showing 23 DEGs generally increased by RHY for ZT4F, ZT4M, ZT14F, and ZT14M.

(D) Zoom of cluster C3 showing 6 DEGs generally decreased by RHY for ZT4F, ZT4M, ZT14F, and ZT14M.

(E) Spatial maps of Log2 gene expression under saline and RHY treatments for female mice shown for Sgk1, Lcn2, Nfkbia, Tsc22d3, and Uba52.

(F) Bar diagram illustrating the number of overlapping and non-overlapping DEGs among ZT4F, ZT4M, ZT14F, and ZT14M.

(G) Table showing the fold change and significance level of the 18 DEGs common in all four comparisons. Hot colors indicate increases by RHY, and cold colors decreases.

(H) Functional analysis of ZT4F, ZT4M, ZT14F and ZT14M DEGs showing enrichment of upstream receptors (top 11) and biological functions (bottom 16) extracted from Ingenuity pathway analysis (IPA). Hot colors indicate pathways predicted to be increased by RHY, and cold colors those decreased. Grey indicates no specific direction. The number of DEGs associated with each specific term is shown. Dotted grey lines indicate the significance threshold for enrichment (FDR < 0.05).

(I) Representation of the protein-protein interaction network of the most enriched transcription factors (i.e., overlapping in 3 comparisons) made together with the 18 DEGs common in the ZT4F, ZT4M, ZT14F and ZT14M comparisons.

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