Fig 1.
Flow chart of data preparation, processing, and analysis.
GSE79768 (atrial fibrillation mRNA dataset), GSE58294 (stroke mRNA dataset), GSE66724 (atrial fibrillation related stroke mRNA dataset), GSE70887 (atrial fibrillation miRNA dataset), GSE129409 (atrial fibrillation circRNA dataset). DEMis (differently expressed miRNAs), DECircs (differently expressed circRNAs), ceRNA (competitive endogenous RNA).
Fig 2.
Identification of differentially expressed genes.
Heatmap of the top 30 differentially expressed genes based on GSE79768 (A), and at < 3 h (B), 5 h (C), 24 h (D) after stroke in GSE58294. The color intensity (from red to green) suggests the higher to lower expression.
Fig 3.
Identification of differentially expressed genes.
Heatmap of the top 30 differentially expressed genes based on A GSE66724, B GSE70887, and C GSE129409. The color intensity (from red to green) suggests the higher to lower expression.
Fig 4.
Sample clustering and network construction of the weighted co-expressed genes.
Clustering dendrogram of 8 AF without Stroke and 8 AF with Stroke (A). The color intensity was proportional to disease status (with or without Stroke). Analysis of the scale independence (B) and the mean connectivity (C) for various soft‑thresholding powers. The soft‑thresholding power of 5 was selected based on the scale‑free topology criterion. Dendrogram clustered was based on a dissimilarity measure (1‑TOM). Gene expression similarity is assessed by a pair‑wise weighted correlation metric and clustered based on a topological overlap metric into modules. Each color below represents one co‑expression module, and every branch stands for one gene (D). The cluster dendrogram of module eigengenes was demonstrated (E).
Fig 5.
The identification of key modules via weighted gene co‑expression network analysis.
Heatmap of the correlation between module eigengenes and the disease status of AF-related Stroke (A). The corresponding correlation coefficient along with P‑value is given in each cell, and each cell is color‑coded by correlation according to the color (legend at right). The turquoise module was most significantly correlated with AF-related Stroke. Scatter plot of module eigengenes in the turquoise module was presented (B). The Venn diagram of genes from the key module and DEGs from GSE66724 was drawn (C).
Fig 6.
PPI network of AF-related DEGs (A), PPI network of Stroke-related DEGs (B), and Venn diagrams of AF-related stroke genes (C) were presented. Red, greater degree. blue, lesser degree.
Fig 7.
Enrichment analysis of key modules.
Gene ontology enrichment analysis in DEG1 (A), DEG2 (B), and DEG3 (C). The significance of enrichment gradually increases from blue to red, and the size of the dots indicates the number of genes contained in the corresponding pathway. ROC curves of hub genes in GSE66724 (D) and GSE58294 (E) were present.
Fig 8.
Nervous and cardiovascular diseases related to hub genes based on the CTD database (A-H), circRNA-miRNA-mRNA network (I).
Table 1.
The Gene Ontology (GO) terms enrichment for hub genes of the AF-related stroke.
Fig 9.
The expression levels of 8 hub genes, miR-198, and hsa_circ_0018657 (n = 3).
*: P < 0.05.