Circular RNA Analysis

The X-axis shows the length of the chromosomes, and the Y-axis indicates the log2 of the median of read density. Blue and green indicate the positive and negative strand respectively.

Pie chart of circRNA classification for sample

Boxplot of TPM for each sample. The x-axis shows the sample names and the y-axis shows the log10(TPM). Each box has five statistical magnitudes (max value, upper quartile, median, lower quartile and min value).

TPM density distribution. The x-axis shows the log10(TPM) and the y-axis shows density. Different colors represent different samples.

Correlation analysis between samples. The scatter diagrams demonstrate the correlation coefficient between samples.

The expression of differential circRNA is visualized by volcano plot. The Volcano plot provides a way to perform a quick visual identification of the circRNA displaying large-magnitude changes which are also statistically significant. The plot is constructed by plotting the FDR (-log10) on the y-axis, and the expression fold change (log2) between the two experimental groups on the x-axis. There are two regions of interest in the plot: those points that are found towards the top of the plot (high statistical significance) and at the extreme left or right (strongly down and up-regulated respectively).

Cluster analysis of differentially expressed circRNA. Hierarchical clustering is based on TPMs, where log2(TPM) is used for clustering. Red color represents circRNA with higher expression, while green color represents circRNA with lower expression. Different columns represent different samples, while different rows represent different circRNA.

Gene ontology (GO - Gene Ontology Consortium, 2000) enrichment analysis is a set of the internationally standardized classification system of gene function description that attempts to identify GO terms that are significantly associated with differentially expressed protein coding genes. GO molecules are divided into three main categories: 1) Cellular Component: used to describe the subcellular structure, location and macromolecular complexes, such as nucleoli, telomere and recognition of the initial complex; 2) Molecular Function: used to describe the gene, gene products, individual functions, such as carbohydrate binding or ATP hydrolase activity; 3) Biological Process: used to describe the products encoded by genes involved in biological processes, such as mitosis or purine metabolism.

KEGG is called Kyoto Encyclopedia of Genes and Genomes, it is the main public database of the pathways. A systematic analysis of the metabolic pathways of gene products and compounds in cells and the database of the function of these gene products (KEGG PATHWAY), drug (KEGG DRUG), disease (KEGG DISEASE), functional model (KEGG MODULE), gene sequence (KEGG GENES) and the genome of the genome (KEGG GENOME) and so on. The KO (KEGG ORTHOLOG) system links the various KEGG annotation systems, and KEGG has developed a complete KO annotation system to annotate genomic or transcriptome functionalities of newly sequenced species.

The scatter plot is a graphical representation of the KEGG enrichment analysis results. In this figure, the degree of KEGG enrichment is measured by rich factor, qvalue, and the number of genes enriched in this pathway. Wherein the rich factor refers to the ratio of the number of differentially expressed genes located in the pathway to the total number of annotated genes located in the pathway. The larger the rich factor, the greater the degree of enrichment. Qvalue is the corrected pvalue after the multiple hypothesis test. The value range of qvalue is [0,1], the closer to zero, the more significant the enrichment is.