Journal: Cancers
Article Title: A Review and In Silico Analysis of Tissue and Exosomal Circular RNAs: Opportunities and Challenges in Thyroid Cancer
doi: 10.3390/cancers14194728
Figure Lengend Snippet: Microarray transcriptomic signature of circRNAs in human papillary thyroid carcinoma. ( A ) Characteristics of six PTC patients were retrieved from the Gene Expression Omnibus database (GSE93522). PTC was compared with their paired contralateral normal thyroid tissues ( B ) Boxplots showing the distribution of the values of the selected samples. Median-centered values are indicated after log transform and quantile normalization. ( C ) Principal component analysis for data exploration. The geometrical projection for samples is based on the similarities and differences in the expression of 2895 circRNAs. Samples are plotted across two coordinates; axis 1 explained 52.1% of the variance, whereas axis 2 demonstrated 17% of the data variability. ( D ) Volcano plot displays statistical significance (−log10 p -value) versus magnitude of change (log2 fold change) in PTC compared with controls. Each dot represents a circRNA. The plot shows 137 significantly differentially expressed circRNAs (DEC): 115 upregulated (red dots) and 22 downregulated (blue dots). Analysis was performed using GEO2R software, with the p -value threshold at <0.05 and log fold changes (FC) at >1. ( E ) Heatmap for the 12 thyroid tissue specimens using the 137 differentially expressed circRNAs. There was an upregulation pattern of genes in patient samples. Clear differentiation of four PTC tissues and incomplete separation of two others are shown. ( F ) Principal component analysis to visualize how samples are related to each other. By using the deregulated genes, a complete demarcation was observed between PTC and normal tissues. Axes 1 and 2 explain 66.6% and 9.7% of the variability, respectively. ( G ) The top-up and downregulated circRNAs in PTC tissues. Derived protein-coding genes from which circRNAs were formed are shown. Fold change values are depicted at the end of the bars. ( H ) Frequency of tested circRNAs in the microarray according to their chromosomal localization. Y axis is log10 transformed, and the X axis represents the human chromosomes with removed missing chromosomes (chromosomes 18, 21, and Y). ( I ) Chromosomal ideograms represent the differentially expressed circRNAs annotated with lines in color at specific base-pair locations: blue for upregulated DECs and green for downregulated DECs.
Article Snippet: The platform used was “GPL19978 Agilent-069978 Arraystar Human CircRNA microarray V1”.
Techniques: Microarray, Expressing, Software, Derivative Assay, Transformation Assay
