Investigation of Potential Molecular Biomarkers for Diagnosis and Prognosis of AFP-Negative HCC

Figures & data

Figure 1 Volcano plots of differentially expressed lncRNA (A), miRNA (B) and mRNA (C) in AFP-negative HCC. Red dots indicate genes significantly upregulated and green indicates genes significantly downregulated.

Table 1 12 DElncRNAs Target 23 DEmiRNAs from the miRcode Database

lncRNA	miRNA
H19	hsa-mir301b	hsa-mir-93	hsa-mir-519d	hsa-mir-206	hsa-mir-216b
LINC00482	hsa-mir-206	hsa-mir-214
FAM99B	hsa-mir-205	hsa-mir-214
FAM99A	hsa-mir-205	hsa-mir-214
LINC00152	hsa-mir-195	hsa-mir-424	hsa-mir-206	hsa-mir-205	hsa-mir-216b
	hsa-mir-31
RUSC1-AS1	hsa-mir-96	hsa-mir-195	hsa-mir-424	hsa-mir-182	hsa-mir-214
	hsa-mir-216a	hsa-mir-216b	hsa-mir-31
MAGI2-AS3	hsa-mir-93	hsa-mir-372	hsa-mir-373	hsa-mir-137	hsa-mir-195
	hsa-mir-424	hsa-mir-204	hsa-mir-214	hsa-mir-216a	hsa-mir-216b
	hsa-mir-217	hsa-mir-508	hsa-mir-31
GAS5	hsa-mir-93	hsa-mir-372	hsa-mir-373	hsa-mir-96	hsa-mir-137
	hsa-mir-182	hsa-mir-205	hsa-mir-21	hsa-mir-216a	hsa-mir-216b
	hsa-mir-217	hsa-mir-221	hsa-mir-222	hsa-mir-31
CRNDE	hsa-mir-183	hsa-mir-205	hsa-mir-216b	hsa-mir-217	hsa-mir-508
	hsa-mir-221	hsa-mir-222	hsa-mir-31
HULC	hsa-mir-137	hsa-mir-204
SNHG1	hsa-mir-137	hsa-mir-195	hsa-mir-424	hsa-mir-182	hsa-mir-206
	hsa-mir-204	hsa-mir-205	hsa-mir-21	hsa-mir-216b	hsa-mir-217
LINC00261	hsa-mir-301b	hsa-mir-182	hsa-mir-183	hsa-mir-206	hsa-mir-204
	hsa-mir-214	hsa-mir-216b	hsa-mir-508	hsa-mir-31

Figure 2 Venn diagram analysis for the intersection set between differentially expressed mRNA in AFP-negative HCC and miRNA target genes.

Figure 3 The lncRNA-miRNA-mRNA ceRNA network in AFP-negative HCC. The diamond represents lncRNA, the square represents miRNA and the circle denotes mRNA. The red nodes indicate upregulated RNAs and the green nodes indicate downregulated RNAs.

Figure 4 The GO enrichment analysis of DEmRNAs in the ceRNA network of AFP-negative HCC.

Figure 5 The enriched KEGG pathway of DEmRNAs in the ceRNA network of AFP-negative HCC.

Figure 6 (A) A PPI network of DEmRNAs involved in the ceRNA network of AFP-negative HCC. Red nodes represent the upregulated DEmRNAs and green nodes represent the downregulated DEmRNAs. (B) The top ten highly interacted hub genes were recognized by cytoHubba.

Figure 7 The ROC curves of the top ten hub genes. The AUC of CCNB1, E2F1, RRM2, MCM4, EZH2, PBK, ATAD2, CCNE1, ESR1, and CHAF1A were 0.954, 0.949, 0.916, 0.848, 0.962, 0.929, 0.816, 0.873, 0.920, and 0.928, respectively.

Figure 8 Kaplan–Meier survival curves of lncRNAs (A and B), miRNA (C–E), mRNA (F and G) associated with overall survival in AFP-negative HCC.