Figure 2.

Identification of recurrence-specific differentially expressed genes. RNA-seq and microRNA-seq analysis of 467 tissue specimens of PTC patients in The Cancer Genome Atlas (TCGA) database integrated with clinical data, pathological data, molecular landscape, and survival information. By comparing the transcriptome signature of 46 recurrent and 441 disease-free patients, we identified a panel of eight deregulated microRNAs and 16 deregulated mRNAs associated with disease recurrence and/or progression. (A) Volcano plot and table showing differentially expressed microRNAs in recurrent cohorts compared with the non-recurrence group. The significance threshold was set at a false discovery rate (FDR) < 0.05 and a |log2 fold change (logFC)| > 1.0. Three upregulated genes in red and five downregulated genes in blue are shown. (B) Volcano plot and table showing differentially expressed mRNAs/lncRNAs in recurrent cohorts compared with the non-recurrence group. Four upregulated genes in red and 12 downregulated genes in blue are shown. (C) Co-expression analysis of genes and miRNAs. Spearman’s correlation analysis was performed. In the correlation matrix, red color shows a positive correlation and blue shows a negative correlation. (D) Functional enrichment analysis of DEGs. (E) Pathway enrichment analysis of DEmiRs using Diana lab tools. Abbreviations: solute carrier family 5 member 5 (SLC5A5), angiotensin II receptor type 1 (AGTR1), transmembrane protein 139 (TMEM139), betaine--homocysteine S-methyltransferase 2 (BHMT2), frizzled class receptor 9 (FZD9), mab-21 like 2 (MAB21L2), glutamate ionotropic receptor kainate type subunit 4 (GRIK4), interaction protein for cytohesin exchange factors 1 (IPCEF1), natriuretic peptide receptor 3 (NPR3), neurotrophin 3 (NTF3), heart and neural crest derivatives expressed 2 (HAND2), gap junction protein beta 6 (GJB6), pregnancy-specific beta-1-glycoprotein 3 (PSG3), matrix metallopeptidase 9 (MMP9), cadherin 4 (CDH4), and collagen type XIX alpha 1 chain (COL19A1).