Fig. 2
Factors influencing gene expression variability of reference-free (RF) data. a Scatter plots showing global gene expression patterns (log2-transformed) between RF and reference-based (RB) approaches in different human tissues with linear regression lines (red color). The ρ value indicates Spearman’s correlation coefficient. b Correlation between expression level consistency and average expression levels obtained by the RB method. Expressed genes are uniformly divided into five groups with top 0–20% (Group 1), 20–40% (Group 2), 40–60% (Group 3), 60–80% (Group 4), and 80–100% (Group 5) of the expressed genes. c Correlation between expression level consistency and average length of the CDS annotated by the reference gene model. d Correlation between expression level consistency and gene family size obtained from reference genome sequence data. Solid lines represent the corresponding linear regression. Spearman’s ρ and p values were calculated using the cor.test function of the stats package in R