2.2. Differential expression analysis of circRNAs, miRNAs and mRNAs

EdgeR [²³] is a package in R that can be used to identify differential expression in count-based expression data using an overdispersed Poisson model and an empirical Bayes method. It was applied for normalization and differential expression analysis of circRNAs, miRNAs and mRNAs between RCC tissues and normal kidney tissues. We filtered out RNAs with an expression count < 1, and the counts for duplicate RNAs were averaged. RNAs with a |Log (fold change (FC))|>2 and statistical p-value < 0.05 were considered differentially expressed RNAs (DERNAs) and included differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs), which were further visualized in volcano plots using the ggplot2 package [²⁴].