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Table 1 Summary of the identified tissue and tissue-unique TF pairs as well as top 5 tissue TF pairs in the 79 human tissues.

From: Identification of interacting transcription factors regulating tissue gene expression in human

Tissue

# tissue TF pair

# tissue Unique TF pair

Top 5 tissue TF pairs

Literature support

Fetal liver

150

17

HNF3:HNF4ALPHA**, MYOGNF1:PPARA*, PPARA:PAX2*, HNF1:OCT4*, CMAF:COUP_DR1*

[4]

Liver

162

18

CEBPGAMMA:HNF4ALPHA**, HNF4ALPHA:HNF4ALPHA**, CEBPGAMMA:CEBPGAMMA*, AIRE:HNF3*, HNF3B:RUSH1A*

[3, 26, 41]

Fetal lung

149

9

CEBP:HNF4ALPHA**, CEBP:CEBPA**, VDR:OCT, CEBPGAMMA:PLZF, FOXJ2:GATA4

[3, 41]

Lung

111

8

EBOX:HNF4ALPHA**, CEBP:ETS**, SP3:WT1*, CACD:CETS1P54, EBOX:SPZ1

[42, 43]

Kidney

173

15

HNF3:HNF4ALPHA**, PPARA:SP3, AP2:HAND1E47, AP2:ER, TEL2:SREBP

[4]

Pancreas

146

14

HNF3:HNF4ALPHA**, AP2:TBP*, DEC:MYOGNF1, GATA4:PAX4*, HNF4ALPHA:YY1

[4]

Pancreatic islets

125

9

SP1:SREBP1**, E2A:ZF5_B*, CP2:CP2, CHOP:OCT1, OCT:RUSH1A

 

Cardiac myocytes

139

12

HNF3:HNF3B**, CEBP:PAX4, POU3F2:PAX4, NFAT:SP3, TST1:SREBP1

[4]

Heart

130

10

MYOGNF1:SP3*, CP2:ZIC3, AP2:TAXCREB, TAL1BETAE47:MAF, FAC1:OCT1

 

Skeletal muscle

121

15

OCT1:SP1**, MYOGNF1:DR4*, NKX25:TBP*, TEL2:ZIC3, AP2ALPHA:CP2

[44]

Smooth muscle

137

10

HMGIY:OCT**, EGR1:MYOGNF1*, TST1:PAX2, AP2:TST1, POU3F2:CEBP

 

Tongue

152

17

CEBP:CEBPA**, HNF4ALPHA:SREBP1, MYOGNF1:VDR*, HIC1:MYOGNF1*, CP2:ZIC3

[41]

Uterus

144

12

AP1:HMGIY**, HAND1E47:ZIC3*, PLZF:YY1*, AIRE:PLZF, SP3:WT

[45]

Uterus corpus

158

17

HMGIY:OCT**, HNF3:MYOGNF1*, CP2:E2A*, NF1:SP1*, OCT4:TGIF

[46]

Ciliary ganglion

149

15

AP1:STAT**, CACD:CETS1P54, MYOGNF1:NFY, CETS1P54:VDR, AP2:OCT4*

[47, 48]

Dorsal root ganglion

155

15

CEBP:CEBPGAMMA**, FOXJ2:DR3, AREB6:FOXJ2, CEBP:TST1*, AP2ALPHA:GEN_INI3_B*

[41]

Spinal cord

144

6

ETS:HMGIY**, HIC1:PPARA*, NKX25:PLZF, PPARA:TBP*, CART1:MYOGNF1

[10]

Superior cervical ganglion

157

15

CEBPGAMMA:HNF4ALPHA**, AP1:PLZF*, ETF:HOXA4*, FAC1:GATA4, DR3:TBP*

[3]

Trigeminal ganglion

166

18

ETS:VDR**, TEL2:SPZ1, MINI19_B:PLZF, AP2ALPHA:PAX4*, CP2:TST1*

[49]

Amygdala

148

7

OCT1:OCT1**, PAX:STAT*, EGR1:PAX2, AP2:CETS1P54*, MRF2:HMGIY

[50, 51]

Caudate nucleus

161

6

CEBPGAMMA:CEBPGAMMA**, ETS:VDR**, AP2ALPHA:KROX*, GATA4:XVENT1, CEBPGAMMA:HMGIY

[41]

Cerebellum

149

11

CEBPGAMMA:HMGIY, VDR:TAXCREB*, OSF2:PAX2, DR4:SPZ1*, FAC1:OCT4*

 

Cerebellum peduncles

123

6

CEBPGAMMA:CEBPGAMMA**, ETS:MYB**, ETS:VDR*, CART1:FAC1, DR4:SPZ1*

[41]

Cingulate cortex

131

3

EBOX:ETS**, ETS:HMGIY**, NKX25:TBP*, MRF2:OCT4* AP2:XVENT1*

[10, 52, 53]

Fetal brain

121

12

ETS:HMGIY**, MINI19_B:SRY*, AHRARNT:VDR*, CACD:TAXCREB*, CDXA:HMGIY

[53]

Globus pallidus

145

8

ETS:VDR**, NKX25:TBP*, NKX25:PAX5, AHRHIF:KROX*, AP2:SREBP*

[49]

Hypotalamus

134

5

ETS:HMGIY**, CEBPGAMMA:CEBPGAMMA**, AP2:PPARA*, AP2:PPARA*, PAX:SREBP1*

[41, 53]

Medulla oblongata

124

3

VDR:TAXCREB*, CEBPGAMMA:HMGIY, AP2:ETF*, MAF:PAX4*, MYOGNF1:ZIC3

 

Occipital lobe

132

6

AP2:XVENT1*, NKX25:TBP*, AP2:PPARA*, AP2ALPHA:KROX*, PAX:STAT*

 

Olfactory bulb

155

7

CEBPA:GRE_C, AP2:TST1*, OCT:TST1*, CEBPGAMMA:HMGIY, AP2:PAX4*

 

Parietal lobe

125

2

EBOX:ETS**, TTF1:VDR, AP2:XVENT1*, NKX25:TBP*, CP2:HIC1

[52]

Pons

160

3

ETS:HMGIY**, OCT1:OCT1**, ETS:VDR**, GATA:GATA4*, AP2:SREBP*

[50, 53]

Prefrontal cortex

131

6

PAX:STAT*, AP2:XVENT1*, CMAF:SP3, TAL1BETAE47:PAX2, AHRHIF:KROX*

 

Subthalamic nucleus

128

5

OCT:PAX5*, NKX25:TBP*, AP2ALPHA:DR4*, AHRHIF:KROX*, CP2:ZIC3

 

Temporal lobe

138

8

AP2:ETF*, PAX3:SP1*, POU3F2:MYOGNF1*, NKX25:TBP*, CETS1P54:HMGIY

 

Thalamus

137

11

PAX:STAT*, CEBPGAMMA:GEN_INI3_B, XVENT1:YY1, MAZ:VMYB, AP2ALPHA:PLZF*

 

Whole brain

130

8

CEBPGAMMA:CEBPGAMMA**, GATA:OCT4*, AP2:PPARA*, AP2:PPARA*, POU3F2:NFAT*

[41]

BM CD105+ endothelial

143

10

OCT:STAT**, CEBPGAMMA:PLZF*, ER:TBP*, GRE_C:PPARA, M YOGNF1:SP1*

[54]

BM CD34+

158

7

ETS:HMGIY**, CEBPGAMMA:PLZF*, ETF:TST1*, ETS:RUSH1A*, TAL1BETAE47:SP3*

[53]

BM CD71+ earlyerythroid

145

8

PAX4:YY1*, GEN_INI3_B:GEN_INI3_B, KROX:NF1*, NF1:SP1*, CP2:CP2

 

BM_CD33+ myeloid

164

16

CEBP:CEBPA**, ETS:VDR**, AP2ALPHA:EGR1* P300:SREBP1, CETS1P54:VDR*

[41, 49]

Bone marrow

154

16

CEBP:CEBPA**, DR4:SPZ1*, AP2:OCT4, VDR:SREBP*, DR3:WT1*

[41]

Lymph node

157

7

MINI19_B:LRF, OCT4:PAX4, CP2:ZIC3, AP2ALPHA:TTF1, TAL1BETAE47:PPARA*

 

PB BDCA4+ dentritic cells

159

9

CEBPA:CEBPGAMMA**, KROX:PPARA*, CEBP:TST1*, TST1:PAX2*, DR3:P300*

[41]

PB CD14+ monocytes

146

9

CEBP:CEBPA**, TFE:TST1*, NF1:PAX8, NF1:ZIC3, MYOGNF1:SP1*

[41]

PB CD19+ Bcells

143

5

HMGIY:OCT**, DBP:TBP*, ETS:HOXA4*, CP2:CP2, RUSH1A:RUSH1A

[46]

PB CD4+ Tcells

161

10

ETS:SP1**, CEBPGAMMA:CEBPGAMMA**, CP2:SZF11, FAC1:VMYB, AREB6:GATA4

[41, 55]

PB CD56+ NKCells

125

10

ETS:GRE_C, CEBPA:CEBPGAMMA**, OCT1:SPZ1* CEBP:TST1*, AP2:GRE_C

[41]

PB CD8+ Tcells

155

8

ETS:SP1**, AREB6:GATA4, AP2ALPHA:MAZ, TTF1:OCT1_07*, KROX:XVENT1*

[55]

Thymus

164

11

EBOX:HNF4ALPHA**, CEBPA:CEBPGAMMA**, AP1:STAT**, ETS:RUSH1A*, TBP:YY1*

[41, 42]

Tonsil

158

10

CEBP:CEBPGAMMA**, NF1:P300, CACD:TAL1BETAE47*, PPARA:SP1*, OSF2:CDXA

[41]

Whole blood

132

8

CEBPGAMMA:CEBPGAMMA**, PPARA:SP3*, ETS:VMYB*, SP3:YY1*, NFAT:PLZF*

[41]

Ovary

127

9

CEBPA:SREBP1, GATA_C:MAF, LRF:NKX25, NF1:ZIC3, CHOP:PAX4

 

Testis

149

9

CEBPGAMMA:CEBPGAMMA**, DR4:SPZ1*, POU3F2:PAX4, MYOGNF1:ZIC3, MYOGNF1:SP1

[41]

Testis germ cell

136

8

HAND1E47:SPZ1*, SP3:WT1, DBP:TBP, TEL2:LRF, POU3F2:COUP_DR1

 

Testis interstitial

115

5

CEBP:CEBPGAMMA**, MYOGNF1:SPZ1*, DR4:SPZ1*, CEBPGAMMA:HMGIY, EBOX:SREBP1

[41]

Testis leydig cell

135

6

MYOGNF1:SPZ1*, FAC1:FOXJ2, TTF1:PPARA, GATA4:RUSH1A, HOXA4:OCT

 

Testis seminiferous tubule

157

9

STAT:STAT**, DR4:SPZ1*, FAC1:FOXJ2, AHRHIF:AP2ALPHA, CMAF:PPARA

[56]

Adrenal cortex

147

17

CEBP:NFAT**, PPARA:SP1, HMGIY:ZF5_B, AP2:TST1, AP2ALPHA:TST1

[57]

Adrenal gland

157

8

PAX3:WT1, PPARA:SP3, TAL1BETAE47:CRX, DR3:SP3, CETS1P54:OCT

 

Fetal thyroid

127

9

CEBPA:CEBPGAMMA**, TST1:PAX2, CART1:PPARA, DR3:SP3, AP2:PPARA

[41]

Pituitary gland

133

19

EBOX:P300, OSF2:YY1, AP2:PPARA, SP3:WT1, EGR1:ZF5_B*

 

Prostate

176

12

CEBPA:ETS**, EBOX:ETS**, ETS:VDR**, AP1:DR3, KROX:NF1

[43, 58]

Salivary gland

132

11

CEBPGAMMA:CEBPGAMMA**, AP2:POU3F2, TTF1:TTF1, CEBPA:CEBPGAMMA, EGR1:P300

[41]

Thyroid

122

11

CEBPA:CEBPGAMMA**, PPARA:SREBP1, GRE_C:SREBP1, MINI19_B:DR3, CMAF:YY1

[41]

721 B lymphoblasts

168

11

CART1:YY1, CP2:ZIC3, HMGIY:PAX4, DBP:TTF1, TEL2:P300

 

Colorectal adenocarcinoma

143

11

FOXJ2:EFC, CART1:HOXA4, MINI19_B:DR4, SP3:WT1, OCT4:PAX2

 

Leukemia chronic myelegenous

151

9

TCF11:NFAT, NCX:PAX2, ETF:SRY, NF1:ZIC3, AP2ALPHA:AREB6

 

Leukemia lymphoblastic

156

17

AP2ALPHA:PAX4, CEBPA:PLZF, AP2ALPHA:TST1, AP2:PPARA, HMGIY:ZF5_B

 

Leukemia promyelocytic

154

6

CEBPGAMMA:CEBPGAMMA**, DR4:SPZ1, CEBPA:FAC1, P300:ZIC3, CP2:ZIC3

[41]

Lymphoma burkitts daudi

147

12

ETS:MYB**, CETS1P54:WT1, CP2:P300, CP2:EBOX, MINI19_B:WT1

[59]

Lymphoma burkitts Raji

131

5

NFAT:OCT1**, PPARA:SP3, E2A:MYOGNF1, CETS1P54:MYB, AREB6:CDPCR3

[60, 61]

Adipocyte

142

14

PPARA:SP1, EGR1:ZF5_B, SP3:SP3, AP2:SRY, PPARA:WT1

 

Appendix

136

8

CEBP:NFAT**, ETS:VDR**, TAL1BETAE47:TEL2, SP3:WT1, DR4:SP3

[57]

Atrioventricular node

140

13

ETS:GRE_C, AREB6:PPARA, ETF:HOXA4, GEN_INI3_B:GEN_INI3_B, AP2:OCT4

 

Bronchial epithelial cells

152

14

TTF1:SP1, POU3F2:GATA4, AP2ALPHA:TTF1, CACD:MAZ, CEBPA:GATA4

 

Placenta

132

5

CEBPA:CEBPGAMMA**, SP3:WT1*, DEC:PAX5, NKX25:STAT1, PPARA:SP1

[41]

Skin

156

20

CEBPA:CEBPGAMMA**, HNF4ALPHA:PPARA, HMGIY:OCT4, CEBPGAMMA:PLZF, AP2ALPHA:CP2

[41]

Trachea

146

12

CEBPA:CEBPGAMMA**, CEBP:PAX4, CETS1P54:PPARA, AP2:XVENT1, AP2ALPHA:TST1

[41]

  1. Top 5 tissue TF pairs are those with the most significant correlation between enriched TFBS pairs and enriched overlapping orthologous genes;
  2. **experimentally proven interacting TFs with literature support; * at least one TF is tissue-specific based on tissue-specific single TFs from TRANSFAC11.4 database [37]