Integrated analysis of lncRNA-associated ceRNA network reveals potential biomarkers for the prognosis of hepatitis B virus-related hepatocellular carcinoma

Figures & data

Figure 1 Hierarchical clustering and heat map analysis of differentially expressed lncRNAs (A), miRNAs (B), and genes (C).

Notes: Each row represents a sample, and each column represents an lncRNA, miRNA, or gene. High- or low-relative expression is displayed as a red or blue strip, respectively. Each group contained 20 different samples.

Abbreviations: T, tumor; N, normal.

Table 1 Differentially expressed genes, miRNAs, and lncRNAs

Symbol	LogFC	FDR	Symbol	LogFC	FDR	Symbol	LogFC	FDR
CDC6	1.05	2.01E–03	hsa-miR-215-3p	29.41	3.08E–06	LINC01662	4.62	1.21E–07
CCNE1	1.02	1.22E–02	hsa-miR-301b	3.80	8.46E–11	DSCR8	4.49	1.73E–17
CDK1	1.04	2.02E–03	hsa-miR-483-3p	3.42	3.40E–09	LINC01976	4.30	7.43E–06
E2F2	1.03	7.83E–03	hsa-miR-410-3p	3.25	1.76E–08	LINC00632	3.70	8.51E–13
BUB1	1.11	6.22E–04	hsa-miR-7974	3.25	3.05E–08	DSCR4	3.63	2.03E–12
CCNB1	1.03	2.17E–03	hsa-miR-483-5p	3.22	2.62E–08	LINC02089	3.50	9.85E–05
SFN	1.54	4.46E–06	hsa-miR-200c-3p	3.17	4.31E–08	MIR2052HG	3.34	4.32E–11
GNG4	1.48	6.54E–05	hsa-miR-183-5p	3.11	6.10E–08	PRNT	2.54	1.17E–03
UBE2C	1.23	2.15E–04	hsa-miR-1910-5p	3.09	4.44E–04	LINC00346	2.02	3.33E–05
GNGT1	2.04	1.49E–05	hsa-miR-493-5p	3.08	8.66E–08	FAM182B	1.30	1.04E–02
KIF4A	1.15	5.96E–04	hsa-miR-139-5p	−2.22	1.49E–04	PACRG-AS3	−1.24	2.72E–02
GNG13	1.40	1.87E–02	hsa-miR-30c-2-3p	−1.59	1.04E–02	LINC01558	−1.59	1.17E–03
PF4	−1.36	2.03E–02	hsa-miR-378i	−1.54	1.32E–02	LINC02312	−1.60	1.47E–03
IL-6	−1.04	2.94E–02	hsa-miR-199a-5p	−1.45	2.11E–02	LINC02453	−1.74	3.36E–04
CXCR1	−1.056	1.64E–02	hsa-miR-30a-5p	−1.45	2.16E–02	LILRB1-AS1	−1.87	0.013104
INS	−3.6	9.75E–11	hsa-miR-125b-5p	−1.43	2.29E–02	LINC01561	−2.05	7.28E–05
RD3L	−3.16	2.70E–10	hsa-miR-378d	−1.43	2.43E–02	LINC01550	−2.09	1.89E–05
VGLL1	−2.96	4.88E–06	hsa-miR-10a-5p	−1.41	2.62E–02	LINC01620	−2.16	2.77E–05
TH	−2.85	7.02E–15	hsa-miR-133a-3p	−1.38	3.15E–02	LINC01554	−2.19	5.61E–06
CLDN8	−2.83	3.13E–06	hsa-miR-101-3p	−1.37	3.12E–02	B3GALT5-AS1	−2.31	3.83E–06

Abbreviations: FC, fold change; FDR, false discovery rate.

Figure 2 Function enrichment analyses for the differentially expressed genes.

Note: (A) GO enrichment and (B) KEGG pathways enrichment.

Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Table 2 GO enrichment for differentially expressed genes using the DAVID database

Category	Term	FDR	Genes
Up	GO:0007049~cell cycle	4.24E–10	E2F1, KIF23, E2F2, KIFC1, XRCC2, E2F7, E2F8, MAEL, PKMYT1, TTK, PTTG1, AURKB, GTSE1, KIF2C, CCNE1, CDCA8, CDC45, CDCA2, PIWIL3, CDCA5, CDC6, CDK1, EGFL6, MND1, PBK, HMGA2, UBE2C, PRDM9, BUB1B, ERN2, NEK2, ANLN, CEP55, SPC24, SPC25, NCAPH, DUSP13, HJURP, NCAPG, CENPA, BUB1, FBXO43, SKA3, SKA1, TRIP13, EXO1, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, CDKN3, CDC25C, CDC25A, GSG2, CCNB1, CCNB2, TEX11
	GO:0022402~cell cycle process	1.13E–11	KIF23, E2F1, KIFC1, XRCC2, MAEL, PKMYT1, TTK, AURKB, PTTG1, GTSE1, CCNE1, KIF2C, CDCA8, CDCA2, PIWIL3, CDCA5, CDC6, CDK1, MND1, PBK, UBE2C, HMGA2, PRDM9, BUB1B, ERN2, NEK2, ANLN, CEP55, SPC24, SPC25, NCAPH, DUSP13, CENPA, NCAPG, FBXO43, BUB1, SKA3, SKA1, TRIP13, EXO1, DLGAP5, KIF18A, NUF2, NDC80, BIRC5, CDC20, CDC25C, CDKN3, CDC25A, CCNB1, CCNB2, TEX11
	GO:0022403~cell cycle phase	1.74E–15	E2F1, KIF23, KIFC1, XRCC2, NEK2, MAEL, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, GTSE1, SPC24, CCNE1, KIF2C, SPC25, NCAPH, CDCA8, DUSP13, NCAPG, BUB1, FBXO43, CDCA2, SKA3, PIWIL3, SKA1, CDCA5, TRIP13, EXO1, CDK1, CDC6, DLGAP5, NUF2, KIF18A, MND1, CDC20, BIRC5, NDC80, PBK, HMGA2, CDKN3, CDC25C, UBE2C, CDC25A, CCNB1, PRDM9, CCNB2, BUB1B, TEX11
	GO:000279~M phase	3.28E–16	KIF23, KIFC1, XRCC2, NEK2, MAEL, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, SPC24, KIF2C, SPC25, NCAPH, CDCA8, DUSP13, NCAPG, BUB1, FBXO43, CDCA2, SKA3, PIWIL3, SKA1, CDCA5, TRIP13, EXO1, CDK1, CDC6, DLGAP5, NUF2, KIF18A, MND1, CDC20, BIRC5, NDC80, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, PRDM9, CCNB2, BUB1B, TEX11
	GO:000278~mitotic cell cycle	2.13E–11	E2F1, KIF23, KIFC1, NEK2, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, GTSE1, SPC24, CCNE1, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, CENPA, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, CDC20, BIRC5, NDC80, PBK, HMGA2, CDKN3, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B
	GO:0007067~mitosis	6.55E–14	KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B
	GO:000280~nuclear division	6.55E–14	KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B
	GO:0000087~M phase of mitotic cell cycle	9.83E–14	KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B
	GO:0048285~organelle fission	1.97E–13	KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B
	GO:0051301~cell division	2.47E–08	KIF23, KIFC1, NEK2, ANLN, CEP55, AURKB, PTTG1, SPC24, CCNE1, SPC25, CDCA8, NCAPH, NCAPG, CDCA2, BUB1, SKA3, POU3F2, SKA1, CDCA5, CDK1, CDC6, NUF2, BIRC5, NDC80, CDC20, HMGA2, UBE2C, CDC25C, CDC25A, CCNB1, CCNB2, BUB1B
Down	GO:0007267~cell–cell signaling	1.82E–07	EDN3, GABRB3, FCRL2, VIPR1, VIPR2, GDNF, WNT2, KCNQ5, WISP2, SLC1A2, GRIN2B, CHRNA4, EFNB3, NPBWR1, IL26, NRXN1, NTSR1, IL22, SIGLEC6, GRM7, WNT9A, DRD1, GRAP, OXT, DRD5, TH, MME, RIMS1, CCL24, INS, CCL21, PRIMA1, BMP3, IL6, PLP1, NOS1, NTF3, DLGAP2, GABRA5, NPY5R, KCNK3, CCL17, WNT7B, CXCL14, PNOC, GRIA1, NTRK2, ADRA1A, SLC5A7, WNT7A, IL2, HTR2A
	GO:0006952~defense response	2.83E–07	KLRC4, KLRC2, KLRC3, CXCR1, CFP, GRIN2B, HAMP, RNASE7, IFNG, XCR1, NLRP7, CAMP, PRG2, PSG3, IL22, NCR1, NCR3, CCR9, PROK2, PSG8, PPBP, CD40LG, GRM7, DEFA3, PLA2G2D, CTSG, NGF, KIR3DL2, CLEC1B, C7, DRD1, CCK, CCL24, AZU1, FCN3, INS, CCL21, FCN2, CNR2, SFTPD, IL1RAPL2, SELP, IL6, IL5, IL1RL1, GABRA5, CCL19, CD5L, STAB2, S100A12, CCL17, MPO, SELE
	GO:0044057~regulation of system process	3.67E–05	BMP10, EDN3, DRD1, CCK, ERBB4, MYL3, EDN2, DRD5, OXT, TH, GDNF, DES, GRIN2B, INS, IFNG, LGI1, ARC, GNAO1, NOS1, NTF3, NPY1R, NPY5R, PROK2, TNNT3, CHRM2, NTRK2, TBXA2R, AVPR1A, IL2, HTR2A, NGF
	GO:0007268~synaptic transmission	1.17E–04	DRD1, GABRB3, DRD5, OXT, TH, VIPR1, RIMS1, WNT2, KCNQ5, SLC1A2, GRIN2B, CHRNA4, PRIMA1, PLP1, NOS1, NTF3, DLGAP2, NPBWR1, GABRA5, NRXN1, NTSR1, NPY5R, KCNK3, PNOC, GRIA1, GRM7, SLC5A7, WNT7A, HTR2A
	GO:0051046~regulation of secretion	1.79E–03	EDN3, IL6, EDN2, OXT, FGF23, NPY1R, GDNF, NPY5R, GCK, GRIN2B, CD40LG, INS, GRM7, IFNG, NTRK2, AVPR1A, CHRNA4, TRPV6, IL2, HTR2A, NGF
	GO:0006935ĉhemotaxis	3.12E–03	EDN3, IL6, EDN2, CXCR1, CCL19, PF4, CCL17, CCR9, AZU1, CCL24, PROK2, PPBP, CXCL14, CCL21, IFNG, SFTPD, XCR1, LECT2
	GO:0042742~defense response to bacterium	8.64E–03	SELP, IL6, CAMP, PRG2, STAB2, S100A12, AZU1, CFP, PPBP, HAMP, RNASE7, IFNG, DEFA3, CTSG
	GO:0050900~leukocyte migration	9.20E–03	AZU1, EDN3, SELP, IL6, EDN2, IFNG, ELANE, SFTPD, PF4, SELE
	GO:0022610~biological adhesion	1.39E–02	CLDN8, CLSTN2, OPCML, DSCAML1, CLDN10, L1CAM, MEGF10, WISP2, SRPX, TNR, DPT, DSCAM, TECTA, SELP, MAG, HAPLN4, RET, CDHR1, PCDH11X, CDHR2, IGFALS, SIGLEC11, AJAP1, STAB2, NRXN1, PCDH19, CTNNA3, CLEC4M, DSG4, LYVE1, FREM3, HEPACAM, SIGLEC6, FREM2, CD40LG, DSG1, CDH19, ITGAD, CNTN3, SELE, COL20A1, IL2
	GO:0006954înflammatory response	2.80E–02	SELP, C7, IL6, IL5, CXCR1, CCL19, IL22, S100A12, CCL17, NCR3, AZU1, CFP, CCL24, PROK2, FCN3, CD40LG, INS, CCL21, FCN2, CNR2, XCR1, SELE, PLA2G2D, NGF

Note: Top 10 terms were listed.

Abbreviations: DAVID, Database for Annotation, Visualization and Integrated Discovery; FDR, false discovery rate; GO, Gene Ontology.

Table 3 KEGG pathway enrichment for differentially expressed genes using the DAVID database

Category	Term	FDR	Genes
Up	hsa04110:cell cycle	2.16E–08	E2F1, E2F2, CDK1, CDC6, PKMYT1, TTK, CDC20, PTTG1, SFN, CDC25C, CDC25A, CCNB1, CCNE1, CDC45, CCNB2, BUB1, BUB1B
	hsa04080:neuroactive ligand–receptor interaction	2.66E–04	GABRD, CGA, GABRG2, GABRA2, GABRA3, GLRA2, LEP, GRM4, SSTR5, KISS1R, HTR1B, GABRR1, GRID2, NPFFR2, TAAR1, HTR1D, GLP1R
	hsa04115:p53 signaling pathway	2.08E–02	CCNB1, CDK1, CCNE1, CCNB2, SFN, GTSE1
	hsa04060:cytokine–cytokine receptor interaction	2.69E–02	LEP, CCR8, CCL20, GDF5, EGF, BMP7, CCL7, IL11, CCL26
	hsa04062:chemokine signaling pathway	2.73E–02	CCR8, GNGT1, CCL20, GNG13, GNG4, CCL7, CCL26
	hsa00604:glycosphingolipid biosynthesis	2.99E–02	ST6GALNAC5, B4GALNT1
	hsa04512:ECM–receptor interaction	3.14E–02	IBSP, COMP, COL2A1, COL11A1
	hsa04350:TGF-beta signaling pathway	3.33E–02	COMP, GDF5, BMP7, PITX2
	hsa03320:PPAR signaling pathway	4.83E–02	LPL, MMP1, FABP6
Down	hsa00830:retinol metabolism	8.15E–10	CYP3A4, CYP1A1, CYP2B6, CYP2C8, ADH1B, CYP26A1, ADH7, CYP1A2, CYP3A43, CYP2A13, CYP4A11, UGT2B17, CYP4A22, LRAT, ADH4, CYP2A6, CYP2A7, RDH16
	hsa00982:drug metabolism	2.89E–05	CYP3A4, CYP2B6, CYP2C8, ADH1B, ADH7, CYP1A2, CYP2E1, GSTM5, CYP3A43, CYP2A13, UGT2B17, ADH4, CYP2A6, CYP2A7
	hsa04080:neuroactive ligand–receptor interaction	1.79E–04	GPR83, DRD1, GABRB3, DRD5, PTH1R, PRSS1, VIPR1, VIPR2, GCGR, GRIN2B, CNR2, GLP2R, GABRP, NPBWR1, GABRA5, NPY1R, NTSR1, NPY5R, GRIA1, CHRM2, GRM7, PTGDR, TBXA2R, AVPR1A, ADRA1A, CTSG, HTR2A
	hsa04060:cytokine–cytokine receptor interaction	2.07E–04	CXCR1, CNTFR, PF4, PF4V1, CCL24, CXCR5, CCL21, IFNG, XCR1, AMHR2, IL6, IL5, FLT3, TNFRSF13B, TNFRSF13C, IL26, CCL19, IL22, CCL17, CCR9, TSLP, CXCL14, PPBP, CD40LG, IL5RA, NGFR, IL2
	hsa00980:metabolism of xenobiotics by CYP/CYP450	3.64E–04	CYP3A43, CYP3A4, UGT2B17, CYP1A1, CYP2B6, ADH4, CYP2C8, ADH1B, ADH7, CYP2E1, CYP1A2, GSTM5
	hsa00232:caffeine metabolism	1.50E–03	CYP2A13, NAT2, CYP2A6, CYP2A7, CYP1A2
	hsa00983:drug metabolism	2.10E–02	CYP3A43, CYP3A4, CYP2A13, UGT2B17, NAT2, UPP2, CYP2A6, CYP2A7
	hsa04340:Hedgehog signaling pathway	2.00E–02	WNT2, WNT1, WNT10A, WNT7B, WNT9A, HHIP, GAS1, WNT7A, BMP5

Abbreviations: DAVID, Database for Annotation, Visualization and Integrated Discovery; FDR, false discovery rate; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 3 Protein and protein interaction network for the differentially expressed genes.

Notes: Red, upregulated; green, downregulated. The larger size of node (protein) indicates the higher degree (interaction relationships) of it.

Abbreviation: FC, fold change.

Figure 4 Modules extracted from the protein and protein interaction network.

Notes: (A) module 1; (B) module 2; (C) module 3; and (D) module 4. Red, upregulated; green, downregulated. The larger size of node (protein) indicates the higher degree (interaction relationships) of it.

Table 4 Topological features for each protein in PPI network

Gene	Degree	Gene	CC	Gene	BC	Gene	APL	Overlapped	Expression
GNGT1	87	IL6	0.3179	IL6	0.2515	IL6	3.1461	CCNB1	Up
GNG13	85	CHRM2	0.2989	UBE2C	0.1845	CHRM2	3.3455	CDK1	Up
GNG4	64	SH3GL2	0.2959	NGF	0.1695	SH3GL2	3.3792	GNG4	Up
CDK1	56	EGF	0.2947	TH	0.1586	EGF	3.3933	UBE2C	Up
CCNB1	52	ESR1	0.2890	GNGT1	0.1413	ESR1	3.4607	GNGT1	Up
CDC20	48	CCL20	0.2848	FOSB	0.1406	CCL20	3.5112	KIF4A	Up
BUB1	48	GNGT1	0.2846	MMP1	0.1388	GNGT1	3.5140	PF4	Down
CCNB2	47	GNG13	0.2823	CHRM2	0.1186	GNG13	3.5421	GNG13	Up
KIF2C	47	INS	0.2821	SH3GL2	0.1164	INS	3.5449
PMCH	45	UBE2C	0.2808	EGF	0.1106	UBE2C	3.5618
AURKB	44	PF4	0.2803	E2F1	0.1043	PF4	3.5674
CENPA	43	PTHLH	0.2786	ESR1	0.1013	PTHLH	3.5899
KIF20A	39	GNG4	0.2777	GNG13	0.0956	GNG4	3.6011
BUB1B	39	NGF	0.2766	INS	0.0904	NGF	3.6152
NCAPG	38	GNAO1	0.2728	KIF4A	0.0670	GNAO1	3.6657
CDCA8	38	KIF4A	0.2722	PTHLH	0.0669	KIF4A	3.6742
GCGR	37	PPBP	0.2713	CDK1	0.0637	PPBP	3.6854
NPSR1	37	GNA14	0.2709	ACAN	0.0632	GNA14	3.6910
BIRC5	37	LEP	0.2707	CCL20	0.0620	LEP	3.6938
TTK	37	TERT	0.2707	GNAO1	0.0593	TERT	3.6938
NDC80	37	GNAZ	0.2669	CAMK2B	0.0547	GNAZ	3.7472
DLGAP5	36	NGFR	0.2661	LPL	0.0444	NGFR	3.7584
UBE2C	35	SYT9	0.2655	CYP19A1	0.0430	SYT9	3.7669
CDC45	35	E2F1	0.2651	CCNB1	0.0417	E2F1	3.7725
PF4	34	HTR1B	0.2645	GNG4	0.0402	HTR1B	3.7809
KIF4A	34	CDK1	0.2639	CHRNA1	0.0394	CDK1	3.7893
PBK	34	PMCH	0.2639	PF4	0.0393	PMCH	3.7893
KIF23	34	HTR1D	0.2639	RHO	0.0370	HTR1D	3.7893
CXCR1	33	CCNB1	0.2625	NOS1	0.0353	CCNB1	3.8090
XCR1	33	CXCR1	0.2597	NGFR	0.0348	CXCR1	3.8511

Note: Top 30 genes were listed.

Abbreviations: APL, average path length; BC, betweenness centrality; CC, closeness centrality; PPI, protein–protein interaction.

Table 5 BinGO enrichment for genes in modules

Module	Description	FDR	Genes in test set
M1	Mitotic cell cycle	9.74E–37	CDCA5|BUB1B|CDCA8|NCAPG|TTK|CENPA|SKA1|AUR KB|CDC20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BU B1|CEP55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18 A|CDK1|BIRC5|KIF2C|SPC24|CDKN3|SPC25
	Nuclear division	9.74E–37	CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25
	Mitosis	9.74E–37	CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25
	M phase of mitotic cell cycle	1.65E–36	CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25
	Organelle fission	1.65E–36	CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25
	M phase	2.75E–36	CDCA5|BUB1B|CDCA8|NCAPG|TTK|SKA1|AURKB|CDC 20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP 55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1 |BIRC5|KIF2C|TRIP13|SPC24|SPC25
	Cell cycle phase	1.03E–35	CDCA5|BUB1B|CDCA8|NCAPG|TTK|SKA1|AURKB|CDC 20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP 55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1 |BIRC5|KIF2C|TRIP13|SPC24|CDKN3|SPC25
	Cell cycle process	5.27E–34	CDCA5|BUB1B|CDCA8|NCAPG|TTK|CENPA|SK A1|AURKB|CDC20|CCNB2|CCNB1|PTTG1|NUF 2|PBK|NEK2|BUB1|CEP55|DLGAP5|UBE2C|KIF 23|NDC80|ANLN|KIF18A|CDK1|BIRC5|KIF2C| TRIP13|SPC24|CDKN3|SPC25
	Cell cycle	7.78E–34	CDCA5|HJURP|BUB1B|CDCA8|NCAPG|TTK|CENPA|SK A1|AURKB|CDC20|CCNB2|CCNB1|CDC45|PTTG1|NU F2|PBK|NEK2|BUB1|CEP55|DLGAP5|UBE2C|KIF23|ND C80|ANLN|KIF18A|CDK1|BIRC5|KIF2C|TRIP13|SPC24| CDKN3|SPC25
	Cell division	8.53E–28	UBE2C|CDCA5|BUB1B|CDCA8|NCAPG|KIF23|SKA1|A URKB|NDC80|CDC20|CCNB2|ANLN|CCNB1|PTTG1| NUF2|CDK1|BIRC5|NEK2|KIF2C|BUB1|CEP55|SPC24 |SPC25
M2	G-protein-coupled receptor protein signaling pathway	4.81E–36	NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|NPBWR1|KISS 1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|XCR1|ED N2|NPY5R|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A| SSTR5|GNG13|PPYR1|PNOC
	Cell surface receptor-linked signaling pathway	8.03E–26	NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|NPBWR1|KISS 1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|XCR1|ED N2|NPY5R|EDN3|GCGR|HTR1D|NPY1R|HTR1B|CCK|A VPR1A|SSTR5|GNG13|PPYR1|PNOC|PF4
	Signaling	6.64E–24	NPFFR2|CHRM2|PMCH|CXCR5|OXT|HTR2A|ADRA1A |GNGT1|GNA14|GRM4|CXCR1|CNR2|GRM7|TBXA2R| GNG4|NPBWR1|KISS1R|CCR9|CCR8|PROK2|TAC3|CCL 19|NTSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3| CCL20|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SST R5|GNG13|APLN|PPYR1|PNOC|GNRH2|PF4
	Behavior	1.44E–23	PMCH|OXT|HTR2A|GRM4|CXCR1|CNR2|KISS1R|CCR 9|CCR8|PROK2|CCL19|NTSR1|XCR1|EDN2|NPY5R|C CL21|EDN3|CCL20|NPY1R|HTR1B|CCK|AVPR1A|PPBP |PPYR1|PF4
	Signaling pathway	3.33E–20	NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|GNG4|NPBW R1|KISS1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|X CR1|EDN2|NPY5R|EDN3|GCGR|HTR1D|NPY1R|HTR1B |CCK|AVPR1A|SSTR5|GNG13|PPYR1|PNOC|PF4
	Signaling process	2.04E–17	CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|GRM7|NPBWR1|KISS1R|PROK2|CCL19|N TSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3|CCL2 0|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SSTR5|G NG13|APLN|PNOC|GNRH2|PF4
	Signal transmission	2.04E–17	CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|GRM7|NPBWR1|KISS1R|PROK2|CCL19|N TSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3|CCL2 0|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SSTR5|G NG13|APLN|PNOC|GNRH2|PF4
	Signal transduction	1.43E–14	CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|KISS1R|PROK2|CCL19|P2RY12|XCR1|ED N2|CCL21|EDN3|CCL20|GCGR|HTR1D|NPY1R|HTR1B| CCK|AVPR1A|SSTR5|GNG13|APLN|PNOC|GNRH2|PF4
	Response to stimulus	2.05E–12	NPFFR2|CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1| GRM4|CXCR1|CNR2|GRM7|GNG4|KISS1R|CCR9|CCR8 |PROK2|CCL19|NTSR1|P2RY12|XCR1|EDN2|NPY5R|C CL21|EDN3|CCL20|GCGR|HTR1D|NPY1R|HTR1B|CCK| AVPR1A|PPBP|GNG13|APLN|PPYR1|PF4
	Response to chemical stimulus	2.96E–11	XCR1|EDN2|CCL21|EDN3|CCL20|GCGR|HTR1D|NP Y1R|HTR1B|OXT|CCK|HTR2A|AVPR1A|PPBP|ADRA1A |GNG13|CXCR1|CNR2|GNG4|CCR9|CCR8|PROK2|CC L19|PF4
M3	Cyclic-nucleotide-mediated signaling	6.43E–09	GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5
	G-protein-coupled receptor protein signaling pathway	2.93E–08	VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTHLH|DR D5|PTGDR
	Second messenger-mediated signaling	9.78E–08	GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5
	G-protein signaling, coupled to cyclic nucleotide second messenger	9.78E–08	VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5
	Cell surface receptor-linked signaling pathway	2.27E–05	VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTHLH|DR D5|PTGDR
	Signaling	3.01E–05	GLP1R|VIPR1|GPR15|VIPR2|GLP2R|PTH1R|DRD1|CGA|T AAR1|PTHLH|DRD5|PTGDR
	Signaling pathway	5.37E–05	GLP1R|VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTH LH|DRD5|PTGDR
	Intracellular signal transduction	8.25E–05	GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5
	Cell–cell signaling	1.41E–04	VIPR1|VIPR2|DRD1|CGA|PTHLH|DRD5
	Signal transduction	1.59E–04	GLP1R|VIPR1|VIPR2|GLP2R|PTH1R|DRD1|CGA|PTHLH |DRD5
	Signaling process	4.51E–04	GLP1R|VIPR1|VIPR2|GLP2R|PTH1R|DRD1|CGA|PTHLH |DRD5
	Cell communication	7.10E–04	VIPR1|VIPR2|DRD1|CGA|PTHLH|DRD5
M4	Drug metabolic process	3.44E–16	CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1|CYP2E1|C YP3A4
	Secondary metabolic process	4.89E–11	CYP26A1|CYP2A6|CYP1A2|CYP1A1|CYP2E1|CYP3A4
	Oxidation reduction	2.91E–10	CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP4A11|CYP1A2|C YP1A1|CYP2E1|CYP3A4
	Steroid metabolic process	4.84E–10	CYP2A6|CYP2B6|CYP1A2|CYP1A1|UGT2B17|CYP2E1| CYP3A4
	Lipid metabolic process	1.79E–09	CYP26A1|CYP2A6|CYP2B6|CYP4A11|CYP1A2|CYP1A1| UGT2B17|CYP2E1|CYP3A4
	Response to drug	1.12E–07	CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1|CYP3A4
	Cellular catabolic process	2.17E–06	CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1| CYP3A4
	Small molecule metabolic process	3.78E–06	CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP4A11|CYP1A2| CYP1A1|CYP3A4
	Cellular lipid metabolic process	6.87E–06	CYP26A1|CYP4A11|CYP1A2|CYP1A1|CYP2E1|CYP3A4
	Catabolic process	9.30E–06	CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1| CYP3A4

Abbreviation: FDR, false discovery rate.

Figure 5 ceRNAs interaction network of lncRNA–miRNA–mRNA.

Notes: Square nodes represent lncRNAs; triangle nodes represent miRNAs; circular nodes represent mRNAs. Red, upregulated; green, downregulated.

Abbreviation: FC, fold change.

Figure 6 HCC-related ceRNAs interaction network of lncRNA–miRNA–mRNA.

Notes: Square nodes represent circRNAs, triangle nodes represent miRNAs, circular nodes represent mRNAs, and rhombus nodes represent HCC pathways. Red, upregulated; green, downregulated.

Abbreviations: FC, fold change; HCC, hepatocellular carcinoma.

Table 6 KEGG pathways for genes in ceRNA network

Term	P-value	Genes
hsa04110:cell cycle	2.85E–06	CCNB1, E2F2, CDK1, CCNE1, CDC6, BUB1, SFN
hsa04115:p53 signaling pathway	0.001617	CCNB1, CDK1, CCNE1, SFN
hsa04080:neuroactive ligand–receptor interaction	0.04606	GPR83, GABRB3
hsa05200:pathways in cancer	0.046995	E2F2, CCNE1

Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 7 Kaplan–Meier analysis to display the correlation of differentially expressed lncRNAs (A), miRNAs (B), and genes (C) with overall survival outcomes for patients with HBV-related HCC.

Abbreviations: HBV, hepatitis B virus; HCC, hepatocellular carcinoma.

Figure 8 Kaplan–Meier analysis to display the correlation of differentially expressed genes with recurrence-free survival outcomes for patients with HBV-related HCC.

Abbreviations: HBV, hepatitis B virus; HCC, hepatocellular carcinoma.

Table 7 Cox regression analysis to screen survival-related genes

ID	Overall survival		Recurrence-free survival
	HR	P-value	HR	P-value
E2F2	1.24	0.049	1.19	0.16
CDC6	1.28	0.0372	1.41	0.0099
CCNE1	1.05	0.0456	1.08	0.32
CDK1	1.32	0.022	1.48	0.0036
BUB1	1.31	0.013	1.37	0.0054
CCNB1	1.4	0.014	1.36	0.023
SFN	1.22	0.0023	1.19	0.0055
hsa-miR-10a-5p	0.882	0.04	0.854	0.27
hsa-miR-125b-5p	0.835	0.019	0.952	0.74
hsa-miR-133a-3p	0.11	0.045	0.879	0.39
hsa-miR-199a-5p	0.986	0.88	0.907	0.28
hsa-miR-30a-5p	0.911	0.0452	0.866	0.32
LINC00346	1.67	0.0051	0.99	0.85
DSCR4	1.03	0.68	0.994	0.95
FAM182B	1.152	0.047	0.84	0.19

Table 8 Confirmation of expressions of crucial lncRNAs, miRNAs, and mRNAs using other datasets

RNA type	Dataset	Symbol	Tumor (mean ± SD)	Control (mean ± SD)	P-value
lncRNA	GSE27462	FAM182B	75.834±27.913	71.793±23.127	0.8096
		LINC00346	124.665±28.955	72.848±14.226	0.01208
	TCGA	FAM182B	3.403±1.255	2.539±0.944	0.081
		LINC00346	14.834±3.436	12.679±1.403	0.0397
miRNA	GSE69580	miR-125b-5p	39.384±23.416	355.428±82.423	0.000606
		miR-10a-5p	4.229±2.103	10.111±2.647	0.00507
	TCGA	miR-125b-5p	8.962±1.092	10.203±0.352	4.09E–08
		miR-10a-5p	13.607±1.198	14.779±0.472	4.89E–06
mRNA	GSE121248	E2F2	4.252±0.181	4.239±0.157	0.696
		CDK1	7.224±1.105	5.379±0.799	2.68793E–16
		CCNE1	7.056±1.032	6.415±0.216	0.00000344
	GSE94660	E2F2	0.83±0.443	0.0611±0.028	1.234E–07
		CDK1	2.141±0.769	0.251±0.121	2.9E–10
		CCNE1	1.412±0.669	0.242±0.129	9.01E–08
	GSE25599	E2F2	0.769±0.496	0.302±0.255	0.01958
		CDK1	5.116±2.925	1.152±0.923	0.005978
		CCNE1	2.015±1.820	0.430±0.242	0.02254
	TCGA	E2F2	5.612±1.296	2.959±1.076	0.000926
		CDK1	8.018±1.428	4.579±1.266	0.00374
		CCNE1	6.322±1.993	3.162±0.979	0.00193

Abbreviation: TCGA, The Cancer Genome Atlas.