Hu and Gallo BMC Genomics 2010, 11:49 http://www.biomedcentral.com/1471-2164/11/49 Page 4 of 15 11 6 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. Tissue # tissue TF # tissue Unique Top 5 tissue TF pairs Literature pair TF pair support Fetal liver 150 17 HNF3:HNF4ALPHA**, MYOGNF1:PPARA*, PPARA:PAX2*, HNF1:OCT4*, CMAF: [4] COUP_DR1* Liver 162 18 CEBPGAMMA:HNF4ALPHA**, HNF4ALPHA:HNF4ALPHA**, CEBPGAMMA: [3,26,41] CEBPGAMMA*, AIRE:HNF3*, HNF3B:RUSH1A* Fetal lung 149 9 CEBP:HNF4ALPHA**, CEBP:CEBPA**, VDR:OCT, CEBPGAMMA:PLZF, FOXJ2: [3,41] GATA4 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: [4] YY1 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: [41] ZIC3 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: [41] GEN_INI3_B* Spinal cord 144 6 ETS:HMGIY**, HIC1:PPARA*, NKX25:PLZF, PPARA:TBP*, CART1:MYOGNF1 [10] Superior cervical 157 15 CEBPGAMMA:HNF4ALPHA**, AP1:PLZF*, ETF:HOXA4*, FAC1:GATA4, DR3:TBP* [3] ganglion 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, [41] CEBPGAMMA:HMGIY Cerebellum 149 CEBPGAMMA:HMGIY, VDR:TAXCREB*, OSF2:PAX2, DR4:SPZ1*, FAC1:OCT4* Cerebellum 123 CEBPGAMMA:CEBPGAMMA**, ETS:MYB**, ETS:VDR*, CART1:FAC1, DR4:SPZ1* [41] peduncles 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: [41,53] SREBP1* Medulla oblongata 124 VDR:TAXCREB*, CEBPGAMMA:HMGIY, AP2:ETF*, MAF:PAX4*, MYOGNF1:ZIC3 Occipital lobe 132 AP2:XVENT1*, NKX25:TBP*, AP2:PPARA*, AP2ALPHA:KROX*, PAX:STAT* Olfactory bulb 155 CEBPA:GRE_C, AP2:TST1*, OCT:TST1*, CEBPGAMMA:HMGIY, AP2:PAX4* Parietal lobe 125 EBOX:ETS**, TTF1:VDR, AP2:XVENT1*, NKX25:TBP*, CP2:HIC1 [52] Pons 160 ETS:HMGIY**, OCT1:OCT1**, ETS:VDR**, GATA:GATA4*, AP2:SREBP* [50,53] Prefrontal cortex 131 PAX:STAT*, AP2:XVENT1*, CMAF:SP3, TAL1BETAE47:PAX2, AHRHIF:KROX* Subthalamic nucleus 128 OCT:PAX5*, NKX25:TBP*, AP2ALPHA:DR4*, AHRHIF:KROX*, CP2:ZIC3 Temporal lobe 138 AP2:ETF*, PAX3:SP1*, POU3F2:MYOGNF1*, NKX25:TBP*, CETS1P54:HMGIY Thalamus 137 PAX:STAT*, CEBPGAMMA:GEN_INI3_B, XVENT1:YY1, MAZ:VMYB, AP2ALPHA: PLZF* Whole brain 130 8 CEBPGAMMA:CEBPGAMMA**, GATA:OCT4*, AP2:PPARA*, AP2:PPARA*, [41] POU3F2:NFAT* BM CD105+ 143 10 OCT:STAT**, CEBPGAMMA:PLZF*, ER:TBP*, GRE_C:PPARA, M YOGNF1:SP1* [54] endothelial BM CD34+ 158 7 ETS:HMGIY**, CEBPGAMMA:PLZF*, ETF:TST1*, ETS:RUSH1A*, TAL1BETAE47: [53] SP3* 3 6 7 2 3 6 5 8 11