Table 1. Open in new tab Matrix RNAi...

Perturbed TRF genes	Knocked down TRF gene
TCF1	ΔΔCT	–2.6208333	–0.4641667	–1.3508333	–0.67	–1.0008333	–0.9491667	–0.865	–1.47625
	ΔΔCT SD	0.2166392	0.3597254	0.364969	0.2155686	0.2728902	0.2039744	0.3655958	0.5987373
	P -value	5.83E–07	0.038143	0.0004084	0.0057176	0.0001371	0.0010823	0.0024617	0.017984
TCF2	ΔΔCT	–1.2591667	–3.0958333	–1.0241667	–0.4608333	0.0908333	–0.21	–0.3291667	–0.9295833
	ΔΔCT SD	0.3568102	0.5012421	0.3536914	0.2335968	0.1490153	0.2488322	0.4580488	0.8778892
	P -value	0.0005702	3.304E–05	0.0194871	0.2262878	0.747752	0.5046373	0.2364003	0.1433739
FOXA1	ΔΔCT	–0.875	0.8333333	–2.8466667	–0.06	–0.285	–0.2558333	0.1216667	–0.3483333
	ΔΔCT SD	0.4781014	0.3389995	0.3731717	0.4891846	0.776543	0.7088416	0.4074505	1.0545216
	P -value	0.0066018	0.0044526	1.261E–05	0.8042594	0.4843524	0.4454617	0.5590495	0.4865551
FOXA2	ΔΔCT	–0.9733333	–0.2275	–0.5408333	–2.0508333	–0.8491667	–0.5416667	0.2816667	–0.38625
	ΔΔCT SD	0.3805009	0.5449734	0.3656555	0.6575634	0.8432209	0.7664658	0.6226645	0.6472584
	P -value	0.0092891	0.4924436	0.1712209	0.0009421	0.0578368	0.2080605	0.420319	0.5361367
FOXA3	ΔΔCT	0.5058333	–0.1616667	–0.9508333	–1.1141667	–4.6725	–0.0908333	–0.3416667	–0.9470833
	ΔΔCT SD	0.4289698	0.4932207	0.5931293	0.494027	0.5595853	0.5556228	0.3918171	0.3815078
	P -value	0.3825842	0.7652557	0.2896109	0.1194374	0.0004207	0.8144588	0.2667267	0.1582385
HNF4A	ΔΔCT	–1.24125	–0.0025	–0.6975	–0.3758333	–0.7408333	–2.6116667	–0.2575	–0.8670833
	ΔΔCT SD	0.1852171	0.2156625	0.3150951	0.2856057	0.3782111	0.1717603	0.3282892	0.6722532
	P -value	3.218E–05	0.9831399	0.0058856	0.031243	0.00296	1.017E–05	0.161717	0.0906656
HNF4G	ΔΔCT	1.8383333	0.4266667	0.9883333	0.3075	0.9508333	1.5033333	–1.9116667	0.59625
	ΔΔCT SD	0.5398501	0.4613782	0.3567134	0.3026379	0.3312446	0.2381943	0.5630444	0.4410708
	P -value	0.0048796	0.1195892	0.0099967	0.1646301	0.0015777	6.017E–05	0.0025926	0.1667225
ONECUT1	ΔΔCT	–2.0233333	1.1308333	–1.3333333	–0.2558333	–0.3725	–0.17	0.5225	–3.4158333
	ΔΔCT SD	0.2820222	0.475604	0.4150655	0.1899603	0.381325	0.3294729	0.339382	0.4198365
	P -value	0.0140675	0.0828868	0.0137168	0.4971287	0.2927379	0.6868694	0.3131551	0.0029555

Perturbed TRF genes

Knocked down TRF gene

TCF1

TCF2

FOXA1

FOXA2

FOXA3

HNF4A

HNF4G

ONECUT1

TCF1

ΔΔCT

–2.6208333

–0.4641667

–1.3508333

–0.67

–1.0008333

–0.9491667

–0.865

–1.47625

ΔΔCT SD

0.2166392

0.3597254

0.364969

0.2155686

0.2728902

0.2039744

0.3655958

0.5987373

P -value

5.83E–07

0.038143

0.0004084

0.0057176

0.0001371

0.0010823

0.0024617

0.017984

TCF2

ΔΔCT

–1.2591667

–3.0958333

–1.0241667

–0.4608333

0.0908333

–0.21

–0.3291667

–0.9295833

ΔΔCT SD

0.3568102

0.5012421

0.3536914

0.2335968

0.1490153

0.2488322

0.4580488

0.8778892

P -value

0.0005702

3.304E–05

0.0194871

0.2262878

0.747752

0.5046373

0.2364003

0.1433739

FOXA1

ΔΔCT

–0.875

0.8333333

–2.8466667

–0.06

–0.285

–0.2558333

0.1216667

–0.3483333

ΔΔCT SD

0.4781014

0.3389995

0.3731717

0.4891846

0.776543

0.7088416

0.4074505

1.0545216

P -value

0.0066018

0.0044526

1.261E–05

0.8042594

0.4843524

0.4454617

0.5590495

0.4865551

FOXA2

ΔΔCT

–0.9733333

–0.2275

–0.5408333

–2.0508333

–0.8491667

–0.5416667

0.2816667

–0.38625

ΔΔCT SD

0.3805009

0.5449734

0.3656555

0.6575634

0.8432209

0.7664658

0.6226645

0.6472584

P -value

0.0092891

0.4924436

0.1712209

0.0009421

0.0578368

0.2080605

0.420319

0.5361367

FOXA3

ΔΔCT

0.5058333

–0.1616667

–0.9508333

–1.1141667

–4.6725

–0.0908333

–0.3416667

–0.9470833

ΔΔCT SD

0.4289698

0.4932207

0.5931293

0.494027

0.5595853

0.5556228

0.3918171

0.3815078

P -value

0.3825842

0.7652557

0.2896109

0.1194374

0.0004207

0.8144588

0.2667267

0.1582385

HNF4A

ΔΔCT

–1.24125

–0.0025

–0.6975

–0.3758333

–0.7408333

–2.6116667

–0.2575

–0.8670833

ΔΔCT SD

0.1852171

0.2156625

0.3150951

0.2856057

0.3782111

0.1717603

0.3282892

0.6722532

P -value

3.218E–05

0.9831399

0.0058856

0.031243

0.00296

1.017E–05

0.161717

0.0906656

HNF4G

ΔΔCT

1.8383333

0.4266667

0.9883333

0.3075

0.9508333

1.5033333

–1.9116667

0.59625

ΔΔCT SD

0.5398501

0.4613782

0.3567134

0.3026379

0.3312446

0.2381943

0.5630444

0.4410708

P -value

0.0048796

0.1195892

0.0099967

0.1646301

0.0015777

6.017E–05

0.0025926

0.1667225

ONECUT1

ΔΔCT

–2.0233333

1.1308333

–1.3333333

–0.2558333

–0.3725

–0.17

0.5225

–3.4158333

ΔΔCT SD

0.2820222

0.475604

0.4150655

0.1899603

0.381325

0.3294729

0.339382

0.4198365

P -value

0.0140675

0.0828868

0.0137168

0.4971287

0.2927379

0.6868694

0.3131551

0.0029555

Perturbed TRF genes	Knocked down TRF gene
TCF1	ΔΔCT	–2.6208333	–0.4641667	–1.3508333	–0.67	–1.0008333	–0.9491667	–0.865	–1.47625
	ΔΔCT SD	0.2166392	0.3597254	0.364969	0.2155686	0.2728902	0.2039744	0.3655958	0.5987373
	P -value	5.83E–07	0.038143	0.0004084	0.0057176	0.0001371	0.0010823	0.0024617	0.017984
TCF2	ΔΔCT	–1.2591667	–3.0958333	–1.0241667	–0.4608333	0.0908333	–0.21	–0.3291667	–0.9295833
	ΔΔCT SD	0.3568102	0.5012421	0.3536914	0.2335968	0.1490153	0.2488322	0.4580488	0.8778892
	P -value	0.0005702	3.304E–05	0.0194871	0.2262878	0.747752	0.5046373	0.2364003	0.1433739
FOXA1	ΔΔCT	–0.875	0.8333333	–2.8466667	–0.06	–0.285	–0.2558333	0.1216667	–0.3483333
	ΔΔCT SD	0.4781014	0.3389995	0.3731717	0.4891846	0.776543	0.7088416	0.4074505	1.0545216
	P -value	0.0066018	0.0044526	1.261E–05	0.8042594	0.4843524	0.4454617	0.5590495	0.4865551
FOXA2	ΔΔCT	–0.9733333	–0.2275	–0.5408333	–2.0508333	–0.8491667	–0.5416667	0.2816667	–0.38625
	ΔΔCT SD	0.3805009	0.5449734	0.3656555	0.6575634	0.8432209	0.7664658	0.6226645	0.6472584
	P -value	0.0092891	0.4924436	0.1712209	0.0009421	0.0578368	0.2080605	0.420319	0.5361367
FOXA3	ΔΔCT	0.5058333	–0.1616667	–0.9508333	–1.1141667	–4.6725	–0.0908333	–0.3416667	–0.9470833
	ΔΔCT SD	0.4289698	0.4932207	0.5931293	0.494027	0.5595853	0.5556228	0.3918171	0.3815078
	P -value	0.3825842	0.7652557	0.2896109	0.1194374	0.0004207	0.8144588	0.2667267	0.1582385
HNF4A	ΔΔCT	–1.24125	–0.0025	–0.6975	–0.3758333	–0.7408333	–2.6116667	–0.2575	–0.8670833
	ΔΔCT SD	0.1852171	0.2156625	0.3150951	0.2856057	0.3782111	0.1717603	0.3282892	0.6722532
	P -value	3.218E–05	0.9831399	0.0058856	0.031243	0.00296	1.017E–05	0.161717	0.0906656
HNF4G	ΔΔCT	1.8383333	0.4266667	0.9883333	0.3075	0.9508333	1.5033333	–1.9116667	0.59625
	ΔΔCT SD	0.5398501	0.4613782	0.3567134	0.3026379	0.3312446	0.2381943	0.5630444	0.4410708
	P -value	0.0048796	0.1195892	0.0099967	0.1646301	0.0015777	6.017E–05	0.0025926	0.1667225
ONECUT1	ΔΔCT	–2.0233333	1.1308333	–1.3333333	–0.2558333	–0.3725	–0.17	0.5225	–3.4158333
	ΔΔCT SD	0.2820222	0.475604	0.4150655	0.1899603	0.381325	0.3294729	0.339382	0.4198365
	P -value	0.0140675	0.0828868	0.0137168	0.4971287	0.2927379	0.6868694	0.3131551	0.0029555

Table 1.

Open in new tab

Matrix RNAi among HNFs

Perturbed TRF genes		Knocked down TRF gene
		TCF1	TCF2	FOXA1	FOXA2	FOXA3	HNF4A	HNF4G	ONECUT1
TCF1	ΔΔCT	–2.6208333	–0.4641667	–1.3508333	–0.67	–1.0008333	–0.9491667	–0.865	–1.47625
	ΔΔCT SD	0.2166392	0.3597254	0.364969	0.2155686	0.2728902	0.2039744	0.3655958	0.5987373
	P -value	5.83E–07	0.038143	0.0004084	0.0057176	0.0001371	0.0010823	0.0024617	0.017984
TCF2	ΔΔCT	–1.2591667	–3.0958333	–1.0241667	–0.4608333	0.0908333	–0.21	–0.3291667	–0.9295833
	ΔΔCT SD	0.3568102	0.5012421	0.3536914	0.2335968	0.1490153	0.2488322	0.4580488	0.8778892
	P -value	0.0005702	3.304E–05	0.0194871	0.2262878	0.747752	0.5046373	0.2364003	0.1433739
FOXA1	ΔΔCT	–0.875	0.8333333	–2.8466667	–0.06	–0.285	–0.2558333	0.1216667	–0.3483333
	ΔΔCT SD	0.4781014	0.3389995	0.3731717	0.4891846	0.776543	0.7088416	0.4074505	1.0545216
	P -value	0.0066018	0.0044526	1.261E–05	0.8042594	0.4843524	0.4454617	0.5590495	0.4865551
FOXA2	ΔΔCT	–0.9733333	–0.2275	–0.5408333	–2.0508333	–0.8491667	–0.5416667	0.2816667	–0.38625
	ΔΔCT SD	0.3805009	0.5449734	0.3656555	0.6575634	0.8432209	0.7664658	0.6226645	0.6472584
	P -value	0.0092891	0.4924436	0.1712209	0.0009421	0.0578368	0.2080605	0.420319	0.5361367
FOXA3	ΔΔCT	0.5058333	–0.1616667	–0.9508333	–1.1141667	–4.6725	–0.0908333	–0.3416667	–0.9470833
	ΔΔCT SD	0.4289698	0.4932207	0.5931293	0.494027	0.5595853	0.5556228	0.3918171	0.3815078
	P -value	0.3825842	0.7652557	0.2896109	0.1194374	0.0004207	0.8144588	0.2667267	0.1582385
HNF4A	ΔΔCT	–1.24125	–0.0025	–0.6975	–0.3758333	–0.7408333	–2.6116667	–0.2575	–0.8670833
	ΔΔCT SD	0.1852171	0.2156625	0.3150951	0.2856057	0.3782111	0.1717603	0.3282892	0.6722532
	P -value	3.218E–05	0.9831399	0.0058856	0.031243	0.00296	1.017E–05	0.161717	0.0906656
HNF4G	ΔΔCT	1.8383333	0.4266667	0.9883333	0.3075	0.9508333	1.5033333	–1.9116667	0.59625
	ΔΔCT SD	0.5398501	0.4613782	0.3567134	0.3026379	0.3312446	0.2381943	0.5630444	0.4410708
	P -value	0.0048796	0.1195892	0.0099967	0.1646301	0.0015777	6.017E–05	0.0025926	0.1667225
ONECUT1	ΔΔCT	–2.0233333	1.1308333	–1.3333333	–0.2558333	–0.3725	–0.17	0.5225	–3.4158333
	ΔΔCT SD	0.2820222	0.475604	0.4150655	0.1899603	0.381325	0.3294729	0.339382	0.4198365
	P -value	0.0140675	0.0828868	0.0137168	0.4971287	0.2927379	0.6868694	0.3131551	0.0029555

Perturbed TRF genes		Knocked down TRF gene
		TCF1	TCF2	FOXA1	FOXA2	FOXA3	HNF4A	HNF4G	ONECUT1
TCF1	ΔΔCT	–2.6208333	–0.4641667	–1.3508333	–0.67	–1.0008333	–0.9491667	–0.865	–1.47625
	ΔΔCT SD	0.2166392	0.3597254	0.364969	0.2155686	0.2728902	0.2039744	0.3655958	0.5987373
	P -value	5.83E–07	0.038143	0.0004084	0.0057176	0.0001371	0.0010823	0.0024617	0.017984
TCF2	ΔΔCT	–1.2591667	–3.0958333	–1.0241667	–0.4608333	0.0908333	–0.21	–0.3291667	–0.9295833
	ΔΔCT SD	0.3568102	0.5012421	0.3536914	0.2335968	0.1490153	0.2488322	0.4580488	0.8778892
	P -value	0.0005702	3.304E–05	0.0194871	0.2262878	0.747752	0.5046373	0.2364003	0.1433739
FOXA1	ΔΔCT	–0.875	0.8333333	–2.8466667	–0.06	–0.285	–0.2558333	0.1216667	–0.3483333
	ΔΔCT SD	0.4781014	0.3389995	0.3731717	0.4891846	0.776543	0.7088416	0.4074505	1.0545216
	P -value	0.0066018	0.0044526	1.261E–05	0.8042594	0.4843524	0.4454617	0.5590495	0.4865551
FOXA2	ΔΔCT	–0.9733333	–0.2275	–0.5408333	–2.0508333	–0.8491667	–0.5416667	0.2816667	–0.38625
	ΔΔCT SD	0.3805009	0.5449734	0.3656555	0.6575634	0.8432209	0.7664658	0.6226645	0.6472584
	P -value	0.0092891	0.4924436	0.1712209	0.0009421	0.0578368	0.2080605	0.420319	0.5361367
FOXA3	ΔΔCT	0.5058333	–0.1616667	–0.9508333	–1.1141667	–4.6725	–0.0908333	–0.3416667	–0.9470833
	ΔΔCT SD	0.4289698	0.4932207	0.5931293	0.494027	0.5595853	0.5556228	0.3918171	0.3815078
	P -value	0.3825842	0.7652557	0.2896109	0.1194374	0.0004207	0.8144588	0.2667267	0.1582385
HNF4A	ΔΔCT	–1.24125	–0.0025	–0.6975	–0.3758333	–0.7408333	–2.6116667	–0.2575	–0.8670833
	ΔΔCT SD	0.1852171	0.2156625	0.3150951	0.2856057	0.3782111	0.1717603	0.3282892	0.6722532
	P -value	3.218E–05	0.9831399	0.0058856	0.031243	0.00296	1.017E–05	0.161717	0.0906656
HNF4G	ΔΔCT	1.8383333	0.4266667	0.9883333	0.3075	0.9508333	1.5033333	–1.9116667	0.59625
	ΔΔCT SD	0.5398501	0.4613782	0.3567134	0.3026379	0.3312446	0.2381943	0.5630444	0.4410708
	P -value	0.0048796	0.1195892	0.0099967	0.1646301	0.0015777	6.017E–05	0.0025926	0.1667225
ONECUT1	ΔΔCT	–2.0233333	1.1308333	–1.3333333	–0.2558333	–0.3725	–0.17	0.5225	–3.4158333
	ΔΔCT SD	0.2820222	0.475604	0.4150655	0.1899603	0.381325	0.3294729	0.339382	0.4198365
	P -value	0.0140675	0.0828868	0.0137168	0.4971287	0.2927379	0.6868694	0.3131551	0.0029555

HepG2 cells were transfected with an individual siRNA species against each of the TRF genes. The total RNA was extracted 48 h after the transfection and used for qRT-PCR. The changes in expression levels (perturbations) were evaluated by ΔΔC _T calculated according to the method described by Livak et al. [Livak, K.J. and Schmittgen, T.D. Methods, 25 , 402–408 (2001)].

Tetraplicated experiments were carried out to obtain the average ΔΔC _T , SD and P -value. Only the edges that provided low SD and P -value were used for drawing a putative perturbation network in Figures 5, 8 and Supplementary Figure 1 .

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