Skip to main content
Fig. 6 | Genome Medicine

Fig. 6

From: Reconstruction of full-length circular RNAs enables isoform-level quantification

Fig. 6

Differential circRNA isoform expression between normal and tumor liver tissues of 20 HCC patients. a A schematic comparison between BSJ-level and isoform-level differential expression analysis. b The number of circRNAs detected from normal and tumor liver tissues of 20 HCC patients. Bars in light color represent the numbers of circRNAs in a certain sample, and bars in dark color represent the numbers of highly expressed circRNAs (> 1 BSJ read per 10 million reads). c The number of circRNAs containing AS events that are detected by CIRI-AS. Light bars represent the circRNAs with one AS event and dark bars correspond to circRNAs containing more than one AS events. Black curved lines represent the total mapped data size for each sample. d Comparison of differential expression analysis between BSJ level (x-axis) and isoform level (y-axis). Each dot denotes a circRNA isoform, with its size representing the expression level and its color representing its relative abundance in the parental circRNA. e circRNAs in panel d can be classified into circRNAs with only one isoform and circRNAs with multiple isoforms. For circRNAs with multiple isoforms, Venn diagrams show the discrepancies of significantly up- or downregulated isoforms between BSJ level and isoform level differential expression analyses. f The average isoform expression fold change between normal and tumor tissues of the top 50 most highly expressed circRNAs that have multiple isoforms. Black dot represents the average fold change of circRNAs at the BSJ-level quantification. The dashed box highlights an example shown in panel g. g An example of alternative splicing switch between normal and tumor samples. CircRNA (chr2:207144264|207162097) locating on the ZDBF2 gene can express four isoforms. Rectangles with different colors represent the cirexons within this circRNA. The green and red histograms on each cirexon represent the normalized sequencing depth in normal and tumor samples, respectively. The curve connected cirexons represents the forward splice junction (FSJ) within this circRNA, and its width is proportional to the read support. The red curve represents the FSJ of the dominant circular isoform. The relative abundance of four circular isoforms is shown in bar plot (bottom). h Expression profiles of eight circRNAs quantified at BSJ and isoform level between normal (left) and tumor (right) tissues across 20 HCC patients. Red and cyan lines represent the expression profile of the major and minor circRNA isoform, respectively. All statistic significances are calculated by Mann–Whitney U test. “**” and “*” represent P < 0.01 and P < 0.05. “n.s.” indicates “not significant”

Back to article page