In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

Table 1 miRNA-mRNA interactions observed in HepG2 and SNU449 cells treated with Sorafenib for 6 and 24 hours

Condition	hsa-miR	log2 (Fold-change)	P value	P-adj	mRNA target	Transcript ID	log2 (Fold-change)	P-adj
HepG2 6 hours	hsa-miR-29b-3p	-1.374	3.23E-02	0.9961	HRK	ENSG00000135116.9	1.967	8.926E-08
HepG2 6 hours	hsa-miR-29b-3p	-1.374	3.23E-02	0.9961	JMY	ENSG00000152409.9	1.105	2.253E-13
HepG2 6 hours	hsa-miR-29b-3p	-1.374	3.23E-02	0.9961	TNFAIP3	ENSG00000118503.15	1.186	4.131E-07
HepG2 6 hours	hsa-miR-19b-3p	-1.277	4.29E-02	0.9961	RORA	ENSG00000069667.16	1.048	1.506E-03
HepG2 6 hours	hsa-miR-19b-3p	-1.277	4.29E-02	0.9961	TNFAIP3	ENSG00000118503.15	1.186	4.131E-07
HepG2 6 hours	hsa-miR-19b-3p	-1.277	4.29E-02	0.9961	ZNF385B	ENSG00000144331.20	1.159	1.233E-02
HepG2 6 hours	hsa-miR-19b-3p	-1.277	4.29E-02	0.9961	ARRDC3	ENSG00000113369.9	1.697	4.636E-30
HepG2 24 hours	hsa-miR-4521	-4.496	1.09E-04	0.1484	MBNL1	ENSG00000152601.17	1.242	2.599E-16
HepG2 24 hours	hsa-miR-7974	-3.432	1.97E-42	0.0000	CREB3 L3	ENSG00000060566.14	1.062	4.001E-06
HepG2 24 hours	hsa-miR-194-3p	-1.463	2.73E-08	0.0000	ARHGAP24	ENSG00000138639.18	1.281	1.186E-08
HepG2 24 hours	hsa-miR-194-3p	-1.463	4.47E-05	0.0020	HOXA1	ENSG00000105991.9	1.192	2.484E-06
HepG2 24 hours	hsa-miR-374a-3p	-1.327	4.47E-05	0.0020	SH3GLB1	ENSG00000097033.14	1.296	1.800E-13
HepG2 24 hours	hsa-miR-374a-3p	-1.327	8.95E-03	0.1859	OXR1	ENSG00000164830.18	1.050	2.089E-08
HepG2 24 hours	hsa-miR-374a-3p	-1.327	8.95E-03	0.1859	GOLGA4	ENSG00000144674.16	1.230	8.419E-03
HepG2 24 hours	hsa-miR-374a-3p	-1.327	8.95E-03	0.1859	ARRDC3	ENSG00000113369.9	2.849	2.203E-41
HepG2 24 hours	hsa-miR-27b-5p	-1.236	8.95E-03	0.1859	OPTN	ENSG00000123240.17	1.531	6.346E-20
HepG2 24 hours	hsa-miR-193b-3p	-1.193	3.74E-04	0.0143	SIAH1	ENSG00000196470.12	1.581	1.144E-38
HepG2 24 hours	hsa-miR-193b-3p	-1.193	2.29E-02	0.3864	LAMC2	ENSG00000058085.15	1.327	2.152E-03
HepG2 24 hours	hsa-miR-3187-3p	-1.169	2.29E-02	0.3864	PLK2	ENSG00000145632.15	1.634	3.009E-08
HepG2 24 hours	hsa-miR-3187-3p	-1.169	3.59E-02	0.4538	ATOH8	ENSG00000168874.13	1.691	6.502E-08
HepG2 24 hours	hsa-miR-374b-3p	-1.064	3.59E-02	0.4538	SMAD7	ENSG00000101665.9	1.999	1.669E-42
HepG2 24 hours	hsa-miR-374b-3p	-1.064	7.47E-03	0.1693	TIRARP	ENSG00000163659.13	1.070	1.555E-18
HepG2 24 hours	hsa-miR-769-5p	-1.058	7.47E-03	0.1693	TFAP4	ENSG00000090447.12	1.010	1.161E-11
HepG2 24 hours	hsa-miR-769-5p	-1.058	8.79E-03	0.1859	FAXDC2	ENSG00000170271.11	1.565	1.249E-13
HepG2 24 hours	hsa-miR-4488	9.059	8.79E-03	0.1859	MELTF	ENSG00000163975.12	-1.085	2.722E-05
SNU 6 hours	hsa-miR-15a-5p	-1.526	9.20E-03	0.6536	CHAC1	ENSG00000128965.13	2.262	5.787E-28
SNU 6 hours	hsa-miR-12135	-1.298	2.11E-02	0.6536	FOXJ1	ENSG00000129654.8	1.240	2.099E-06
SNU 24 hours	hsa-miR-29b-1-5p	-2.126	2.50E-05	0.0007	HEY1	ENSG00000164683.17	1.692	2.304E-07
SNU 24 hours	hsa-miR-374c-5p	-1.884	5.25E-03	0.0787	CEBPB	ENSG00000172216.6	1.002	5.306E-17
SNU 24 hours	hsa-miR-374c-5p	-1.884	5.25E-03	0.0787	VEGFA	ENSG00000112715.22	1.448	2.131E-45
SNU 24 hours	hsa-miR-374c-5p	-1.884	5.25E-03	0.0787	ADM	ENSG00000148926.10	2.340	1.782E-143
SNU 24 hours	hsa-miR-32-3p	-1.821	9.41E-04	0.0175	YOD1	ENSG00000180667.10	1.658	1.063E-111
SNU 24 hours	hsa-miR-32-3p	-1.821	9.41E-04	0.0175	TNFAIP3	ENSG00000118503.15	2.316	3.471E-10
SNU 24 hours	hsa-let-7b-3p	-1.541	1.72E-02	0.1785	KLF4	ENSG00000136826.15	1.572	1.166E-31
SNU 24 hours	hsa-let-7b-3p	-1.541	1.72E-02	0.1785	ADRB2	ENSG00000169252.5	1.743	9.094E-48
SNU 24 hours	hsa-miR-195-5p	-1.456	1.51E-02	0.1770	VEGFA	ENSG00000112715.22	1.448	2.131E-45
SNU 24 hours	hsa-miR-195-5p	-1.456	1.51E-02	0.1770	ADRB2	ENSG00000169252.5	1.743	9.094E-48
SNU 24 hours	hsa-miR-34a-5p	-1.316	2.62E-02	0.2364	KLF4	ENSG00000136826.15	1.572	1.166E-31
SNU 24 hours	hsa-miR-34a-5p	-1.316	2.62E-02	0.2364	HSPA1B	ENSG00000204388.7	1.676	2.822E-82
SNU 24 hours	hsa-miR-5701	1.535	3.44E-02	0.2740	SYNGR3	ENSG00000127561.15	-1.505	1.627E-08
SNU 24 hours	hsa-miR-5701	1.535	3.44E-02	0.2740	RFLNB	ENSG00000183688.4	-1.340	1.864E-27
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	ACVR2B	ENSG00000114739.14	-1.075	3.211E-13
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	NR4A2	ENSG00000153234.14	-1.754	9.174E-06
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	CSPG5	ENSG00000114646.10	-1.089	1.709E-08
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	AREG	ENSG00000109321.11	-1.016	2.623E-03
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	NRARP	ENSG00000198435.4	-1.763	3.743E-12
SNU 24 hours	hsa-miR-12136	3.334	4.93E-16	0.0000	MAF	ENSG00000178573.7	-1.748	5.311E-04
SNU 24 hours	hsa-miR-4492	8.427	4.75E-12	0.0000	IGFBP5	ENSG00000115461.5	-1.073	2.379E-18
SNU 24 hours	hsa-miR-4488	13.091	1.08E-32	0.0000	PDGFB	ENSG00000100311.17	-1.101	1.086E-51

Table 2 Predicted interactions between miRNAs and mRNAs, and between their corresponding lncRNAs in HepG2 and SNU449 cells treated with Sorafenib for 6 and 24 hours

Condition	miRNA	log2 (Fold-change)	Target	Target type	Transcript ID	log2 (Fold-change)	P-adj
HepG2 6 hours	hsa-miR-19b-3p	-1.277	RORA	mRNA	ENSG00000069667.16	1.048	1.51E-03
HepG2 6 hours	hsa-miR-19b-3p	-1.277	TNFAIP3	mRNA	ENSG00000118503.15	1.186	4.13E-07
HepG2 6 hours	hsa-miR-19b-3p	-1.277	ZNF385B	mRNA	ENSG00000144331.20	1.159	1.23E-02
HepG2 6 hours	hsa-miR-29b-3p	-1.374	HRK	mRNA	ENSG00000135116.9	1.967	8.93E-08
HepG2 6 hours	hsa-miR-29b-3p	-1.374	JMY	mRNA	ENSG00000152409.9	1.105	2.25E-13
HepG2 6 hours	hsa-miR-29b-3p	-1.374	TNFAIP3	mRNA	ENSG00000118503.15	1.186	4.13E-07
HepG2 24 hours	hsa-miR-193b-3p	-1.193	CYTOR	lncRNA	ENSG00000222041.11	1.421	7.45E-21
HepG2 24 hours	hsa-miR-193b-3p	-1.193	MIR4435-2HG	lncRNA	ENSG00000172965.16	1.204	7.19E-10
HepG2 24 hours	hsa-miR-193b-3p	-1.193	PCBP2-OT1	lncRNA	ENSG00000282977.1	1.086	8.35E-03
HepG2 24 hours	hsa-miR-193b-3p	-1.193	ZFAS1	lncRNA	ENSG00000177410.13	1.413	4.96E-35
HepG2 24 hours	hsa-miR-193b-3p	-1.193	SIAH1	mRNA	ENSG00000196470.12	1.581	1.14E-38
HepG2 24 hours	hsa-miR-193b-3p	-1.193	LAMC2	mRNA	ENSG00000058085.15	1.327	2.15E-03
HepG2 24 hours	hsa-miR-3187-3p	-1.169	MIR4435-2HG	lncRNA	ENSG00000172965.16	1.204	7.19E-10
HepG2 24 hours	hsa-miR-3187-3p	-1.169	DANT2	lncRNA	ENSG00000235244.4	1.014	1.37E-02
HepG2 24 hours	hsa-miR-3187-3p	-1.169	PLK2	mRNA	ENSG00000145632.15	1.634	3.01E-08
HepG2 24 hours	hsa-miR-3187-3p	-1.169	ATOH8	mRNA	ENSG00000168874.13	1.691	6.50E-08
HepG2 24 hours	hsa-miR-374a-3p	-1.327	MIR4435-2HG	lncRNA	ENSG00000172965.16	1.204	7.19E-10
HepG2 24 hours	hsa-miR-374a-3p	-1.327	OXR1	mRNA	ENSG00000164830.18	1.050	2.09E-08
HepG2 24 hours	hsa-miR-374a-3p	-1.327	GOLGA4	mRNA	ENSG00000144674.16	1.230	8.42E-03
HepG2 24 hours	hsa-miR-374a-3p	-1.327	ARRDC3	mRNA	ENSG00000113369.9	2.849	2.20E-41
HepG2 24 hours	hsa-miR-374b-3p	-1.064	THAP9-AS1	lncRNA	ENSG00000251022.6	1.954	2.61E-55
HepG2 24 hours	hsa-miR-374b-3p	-1.064	MALAT1	lncRNA	ENSG00000251562.8	1.024	2.38E-10
HepG2 24 hours	hsa-miR-374b-3p	-1.064	SMAD7	mRNA	ENSG00000101665.9	1.999	1.67E-42
HepG2 24 hours	hsa-miR-374b-3p	-1.064	TIRARP	mRNA	ENSG00000163659.13	1.070	1.55E-18
HepG2 24 hours	hsa-miR-769-5p	-1.058	MALAT1	lncRNA	ENSG00000251562.8	1.024	2.38E-10
HepG2 24 hours	hsa-miR-769-5p	-1.058	SNHG17	lncRNA	ENSG00000196756.13	1.093	1.46E-10
HepG2 24 hours	hsa-miR-769-5p	-1.058	TFAP4	mRNA	ENSG00000090447.12	1.010	1.16E-11
HepG2 24 hours	hsa-miR-769-5p	-1.058	FAXDC2	mRNA	ENSG00000170271.11	1.565	1.25E-13
HepG2 24 hours	hsa-miR-4521	-4.496	MBNL1	mRNA	ENSG00000152601.17	1.242	2.60E-16
HepG2 24 hours	hsa-miR-7974	-3.432	CREB3 L3	mRNA	ENSG00000060566.14	1.062	4.00E-06
HepG2 24 hours	hsa-miR-194-3p	-1.463	ARHGAP24	mRNA	ENSG00000138639.18	1.281	1.19E-08
HepG2 24 hours	hsa-miR-194-3p	-1.463	HOXA1	mRNA	ENSG00000105991.9	1.192	2.48E-06
HepG2 24 hours	hsa-miR-27b-5p	-1.236	OPTN	mRNA	ENSG00000123240.17	1.531	6.35E-20
HepG2 24 hours	hsa-miR-4488	9.059	MELTF	mRNA	ENSG00000163975.12	-1.085	2.72E-05
SNU 6 hours	hsa-miR-15a-5p	-1.526	CHAC1	mRNA	ENSG00000128965.13	2.262	5.79E-28
SNU 6 hours	hsa-miR-12135	-1.298	FOXJ1	mRNA	ENSG00000129654.8	1.240	2.10E-06
SNU 24 hours	hsa-miR-29b-1-5p	-2.126	HEY1	mRNA	ENSG00000164683.17	1.692	2.30E-07
SNU 24 hours	hsa-miR-374c-5p	-1.884	CEBPB	mRNA	ENSG00000172216.6	1.002	5.31E-17
SNU 24 hours	hsa-miR-374c-5p	-1.884	VEGFA	mRNA	ENSG00000112715.22	1.448	2.13E-45
SNU 24 hours	hsa-miR-374c-5p	-1.884	ADM	mRNA	ENSG00000148926.10	2.340	1.78E-143
SNU 24 hours	hsa-miR-374c-5p	-1.884	GAS5	lncRNA	ENSG00000234741.8	1.795	2.73E-202
SNU 24 hours	hsa-miR-374c-5p	-1.884	SNHG5	lncRNA	ENSG00000203875.12	1.370	1.13E-50
SNU 24 hours	hsa-miR-374c-5p	-1.884	SNHG20	lncRNA	ENSG00000234912.12	1.176	1.34E-23
SNU 24 hours	hsa-miR-32-3p	-1.821	YOD1	mRNA	ENSG00000180667.10	1.658	1.06E-111
SNU 24 hours	hsa-miR-32-3p	-1.821	TNFAIP3	mRNA	ENSG00000118503.15	2.316	3.47E-10
SNU 24 hours	hsa-let-7b-3p	-1.541	KLF4	mRNA	ENSG00000136826.15	1.572	1.17E-31
SNU 24 hours	hsa-let-7b-3p	-1.541	ADRB2	mRNA	ENSG00000169252.5	1.743	9.09E-48
SNU 24 hours	hsa-let-7b-5p	-1.541	SNHG12	lncRNA	ENSG00000197989.14	1.092	1.50E-21
SNU 24 hours	hsa-let-7b-5p	-1.541	LMCD1-AS1	lncRNA	ENSG00000227110.7	1.189	5.83E-03
SNU 24 hours	hsa-let-7b-5p	-1.541	CARMN	lncRNA	ENSG00000249669.10	1.637	1.11E-04
SNU 24 hours	hsa-miR-195-5p	-1.456	VEGFA	mRNA	ENSG00000112715.22	1.448	2.13E-45
SNU 24 hours	hsa-miR-195-5p	-1.456	ADRB2	mRNA	ENSG00000169252.5	1.743	9.09E-48
SNU 24 hours	hsa-miR-195-5p	-1.456	SNHG12	lncRNA	ENSG00000197989.14	1.092	1.50E-21
SNU 24 hours	hsa-miR-195-5p	-1.456	EPB41 L4A-AS1	lncRNA	ENSG00000224032.7	2.170	4.36E-34
SNU 24 hours	hsa-miR-195-5p	-1.456	AZIN1-AS1	lncRNA	ENSG00000253320.7	1.070	2.01E-03
SNU 24 hours	hsa-miR-195-5p	-1.456	PVT1	lncRNA	ENSG00000249859.11	1.264	4.13E-79
SNU 24 hours	hsa-miR-195-5p	-1.456	LINC01578	lncRNA	ENSG00000272888.7	1.446	4.59E-72
SNU 24 hours	hsa-miR-34a-5p	-1.316	KLF4	mRNA	ENSG00000136826.15	1.572	1.17E-31
SNU 24 hours	hsa-miR-34a-5p	-1.316	HSPA1B	mRNA	ENSG00000204388.7	1.676	2.82E-82
SNU 24 hours	hsa-miR-34a-5p	-1.316	SNHG7	lncRNA	ENSG00000233016.7	1.116	1.01E-40
SNU 24 hours	hsa-miR-5701	1.535	SYNGR3	mRNA	ENSG00000127561.15	-1.505	1.63E-08
SNU 24 hours	hsa-miR-5701	1.535	RFLNB	mRNA	ENSG00000183688.4	-1.340	1.86E-27
SNU 24 hours	hsa-miR-12136	3.334	ACVR2B	mRNA	ENSG00000114739.14	-1.075	3.21E-13
SNU 24 hours	hsa-miR-12136	3.334	NR4A2	mRNA	ENSG00000153234.14	-1.754	9.17E-06
SNU 24 hours	hsa-miR-12136	3.334	CSPG5	mRNA	ENSG00000114646.10	-1.089	1.71E-08
SNU 24 hours	hsa-miR-12136	3.334	AREG	mRNA	ENSG00000109321.11	-1.016	2.62E-03
SNU 24 hours	hsa-miR-12136	3.334	NRARP	mRNA	ENSG00000198435.4	-1.763	3.74E-12
SNU 24 hours	hsa-miR-12136	3.334	MAF	mRNA	ENSG00000178573.7	-1.748	5.31E-04
SNU 24 hours	hsa-miR-4492	8.427	IGFBP5	mRNA	ENSG00000115461.5	-1.073	2.38E-18
SNU 24 hours	hsa-miR-4488	13.091	PDGFB	mRNA	ENSG00000100311.17	-1.101	1.09E-51

Table 3 Summary of lncRNA-miRNA-mRNA interactions in HepG2 and SNU449 cells at 24 hours of Sorafenib treatment

lncRNA	miRNA	mRNA	Condition
MIR4435-2HG	hsa-miR-3187-3p	ATOH8	HepG2 24 hours
MALAT1	hsa-miR-769-5p	FAXDC2
ZFAS1	hsa-miR-193b-3p	SIAH1
THAP9-AS1	hsa-miR-374b-3p	SMAD7
MALAT1	hsa-miR-374b-3p
MALAT1	hsa-miR-769-5p	TFAP4
SNHG17	hsa-miR-769-5p
MALAT1	hsa-miR-374b-3p	TIPARP
SNHG12	hsa-let-7b-5p	ADRB2	SNU449 24 hours
EPB41 L4A-AS1	hsa-miR-195-5p
PVT1	hsa-miR-195-5p
LINC01578	hsa-miR-195-5p
GAS5	hsa-miR-374c-5p	CEBPB
SNHG5	hsa-miR-374c-5p
SNHG7	hsa-miR-34a-5p	KLF4
EPB41 L4A-AS1	hsa-miR-195-5p	VEGFA
PVT1	hsa-miR-195-5p
LINC01578	hsa-miR-195-5p
GAS5	hsa-miR-374c-5p
SNHG5	hsa-miR-374c-5p