Fig. 2: Genome-wide discovery of ESCC-associated lncRNA biomarkers in the SCH discovery cohort.

A Volcano plot showing the log2(fold change) of significantly differentially expressed lncRNAs (FDR-adjusted p-value of two-sided Wald test < 0.05 and absolute log2-transformed fold-change > 1) between ESCC tissues from non-cancerous tissues. B Heatmap of unsupervised hierarchical clustering of significantly differentially expressed lncRNAs. C Boxplots showing expression levels of six lncRNA biomarkers. For the boxplot, the center line indicates the median; box limits indicate the first and third quartiles; whiskers encompass the 1.5× interquartile range. P values were determined by two-tailed paired t-tests without adjustments for multiple comparisons. D KEGG pathway and GO terms enrichment analysis for mRNAs co-expressed with six lncRNA biomarkers. Jaccard’s similarity index was used to measure the pairwise similarities of the enriched GO terms and KEGG pathways. GO terms and pathways with high Jaccard’s similarity index are considered similar and clustered into five subsets using the ward.D method. The size of the nodes represents the number of analyzed genes contained in the GO terms or KEGG pathways, and the color represents the FDR-adjusted p-value of the enrichment. P-values were determined by FDR-adjusted p-values of a one-sided version of Fisher’s exact test. ESCC, esophageal squamous cell carcinoma; lncRNAs long non-coding RNAs, FDR false discovery rate, ANT adjacent normal tissues.