Human TF List

From GersteinInfo

Here is the list with various gene names mapped.

Citation: Bhardwaj, N., Carson, M. B., Abyzov, A., Yan, K-K., Lu, H. and Gerstein M. B. (2010) Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets, PLoS Comp Biol (in press).

Please read the following before using the file:

Why are there more than one entries sometime for one TF?

This list was compiled by cross-referencing various databases with other with BioMart as the main source. Many of these databases don’t have one-to-one mapping for various TFs. So, I am listing all the mappings for each TF. That's there are many entries against one TF. Probably, the primary reason for this is that the multiple entries are splice-variants of the same TF. Hence, multiple entries.

What does the first set of values indicate (Columns L through O)?

These values are the normalized values obtained by normalizing (using Quantile Normalization) across different *REPLICATES* in the same cell line.

Why are the values so different across different cell lines?

Bot much information is available about the sources of the experimental data, but we believe the conditions in which these values were obtained across different cell lines were different. For example, the experimental protocol, background settings, ways in which these intensity values were recorded, etc. However, since we are mainly interested in the relative expression of these TFs *WITHIN* a cell line, difference in magnitude of the intensity values across these cell lines should not be a problem. Nonetheless, a simple z-score fashion normalization across these cell lines was performed(see below for the next set of normalized values).

What do 1's and -'s indicate (Columns P through S)?

These just indicate if the TF is present (1) or absent (-) in a given cell line. Just to keep a count of how many cell lines a TF is present in.

What does the second set of values indicate (Columns T through W)?

These values are obtained by further normalizing each TF across different cell lines in a Z-score fashion. New value = (old value - Mean of the entire data)/Std Deviation of the entire data

How much can the Z-score fashion normalization be trusted?

Not much. These values from different cell lines are coming from experiments done prossibly under drastically different conditions in diff labs. So, not sure how much sense does it make to do a z-score normalization. Moreover, Z-score works best when the data follows normal distribution. This one probably doesn't.

Quick list of the TFs in Common name format.

ABL1 ACTL6A AFF3 AHR AIRE ALX1 ALX3 ALX4 APC APEX1 AR ARID3A ARNT ARNT2 ARNTL ARNTL2 ATF1 ATF2 ATF3 ATF4 ATF5 ATF6 ATF7 ATOH1 BACH1 BACH2 BARHL2 BCL3 BCL6 BHLHB2 BHLHB3 BIN1 BNC1 BRCA1 BRCA2 BRIP1 BRPF1 CBFB CCNH CCNT1 CCNT2 CDC2 CDK2 CDK7 CDK9 CDX1 CDX2 CDX4 CEBPB CEBPD CEBPE CEBPG CEBPZ CIITA CLOCK CREB1 CREB5 CREBBP CRTC1 CRTC2 CRTC3 CRX CSDA CTBP1 CTCF CTNNB1 CUTL1 CUTL2 DBP DDB1 DDB2 DDIT3 DLX1 DLX2 DLX3 DLX4 DNMT1 DR1 E2F1 E2F2 E2F3 E2F4 E2F5 EGR1 EGR2 EGR3 EGR4 ELF1 ELF3 ELF5 ELK1 ELK3 ELK4 EMX2 EN1 EN2 EOMES EP300 EPAS1 ERCC2 ERCC3 ERCC8 ERF ERG ESR1 ESR2 ESRRA ESRRB ESRRG ETS1 ETS2 ETV1 ETV4 ETV5 ETV6 ETV7 EVI1 EVX1 EWSR1 EZH1 EZH2 FEV FGF3 FKHL18 FLI1 FOS FOSB FOSL1 FOSL2 FOXA1 FOXA2 FOXA3 FOXB1 FOXC1 FOXC2 FOXD2 FOXD3 FOXD4 FOXE1 FOXE3 FOXF2 FOXG1 FOXH1 FOXI1 FOXJ1 FOXJ2 FOXJ3 FOXK2 FOXL1 FOXL2 FOXM1 FOXN3 FOXO1 FOXO3 FOXO4 FOXP1 FOXP2 FOXP3 FOXP4 FOXQ1 GABPA GABPB2 GATA1 GATA2 GATA3 GATA4 GATA6 GBX1 GBX2 GCN5L2 GLI1 GLI3 GLIS2 GMEB1 GRHL1 GSC GSCL GTF2A1 GTF2A1L GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2I GZF1 HAND1 HDAC1 HDAC2 HDAC3 HDAC4 HDAC5 HES1 HES2 HESX1 HEY1 HEY2 HEYL HHEX HIC1 HIF1A HIVEP2 HLF HLX HMGA1 HMGB1 HMGB2 HNF1A HNF1B HNF4A HNRNPA1 HOXA1 HOXA10 HOXA11 HOXA13 HOXA2 HOXA3 HOXA4 HOXA5 HOXA6 HOXA7 HOXA9 HOXB1 HOXB13 HOXB2 HOXB3 HOXB4 HOXB5 HOXB6 HOXB7 HOXB8 HOXB9 HOXC10 HOXC11 HOXC12 HOXC13 HOXC4 HOXC5 HOXC6 HOXC8 HOXC9 HOXD10 HOXD12 HOXD3 HOXD4 HOXD8 HOXD9 HSBP1 HSF1 HSF2 HSF4 ID1 ID2 ID3 IGFBP1 IKZF1 IKZF2 IKZF3 ING1 INSM1 IRF1 IRF2 IRF3 IRF4 IRF5 IRF6 IRF7 IRF8 IRF9 IRX2 IRX3 IRX4 IRX5 IRX6 JUN JUNB JUND KCNIP1 KCNIP2 KCNIP3 KLF1 KLF10 KLF11 KLF12 KLF13 KLF15 KLF16 KLF2 KLF4 KLF5 KLF6 KLF7 KLF9 LBX1 LDB2 LEF1 LHX1 LHX2 LHX3 LHX4 LHX5 LITAF LMO2 LMO3 LYL1 MAF MAFA MAFB MAFF MAFG MAFK MAML1 MAPK8IP1 MAZ MECP2 MED21 MEF2A MEF2B MEF2C MEF2D MEIS1 MEOX1 MEOX2 MIXL1 MLL MLX MLXIP MLXIPL MNAT1 MNT MNX1 MSC MSX2 MTA2 MTF1 MXD1 MXI1 MYB MYBBP1A MYBL1 MYBL2 MYC MYCBP MYCL1 MYCN MYF5 MYF6 MYOCD MYOD1 MYOG MYT1 MZF1 NAT10 NCOA1 NCOA2 NCOA3 NCOA6 NCOR1 NCOR2 NEUROD1 NEUROD2 NEUROG1 NEUROG3 NF1 NFAT5 NFATC2 NFATC3 NFATC4 NFE2 NFE2L1 NFE2L2 NFE2L3 NFIB NFKB2 NFKBIA NFKBIB NFYA NFYB NHLH1 NHLH2 NKRF NKX2-1 NKX2-2 NKX2-5 NKX2-8 NKX3-1 NKX3-2 NKX6-1 NKX6-2 NME2 NMI NONO NPAS1 NPAS2 NR0B1 NR0B2 NR1D1 NR1D2 NR1H2 NR1H3 NR1I2 NR2E1 NR2E3 NR2F1 NR2F2 NR2F6 NR3C1 NR3C2 NR4A1 NR4A2 NR4A3 NR5A1 NR5A2 NR6A1 NRF1 NRL OLIG1 OLIG2 ONECUT1 ONECUT2 OTX1 OTX2 PAX1 PAX2 PAX3 PAX5 PAX6 PAX7 PAX8 PAX9 PBX1 PBX2 PBX2_HUMAN PBX3 PCAF PCGF2 PDX1 PFDN5 PGBD3 PGR PHOX2A PHOX2B PITX1 PITX2 PITX3 PKNOX1 PKNOX2 PLAGL1 PLAGL2 PML PO5F1_HUMAN POU1F1 POU2AF1 POU2F1 POU2F3 POU3F1 POU3F2 POU3F3 POU3F4 POU4F1 POU4F3 POU5F1 POU6F1 PPARA PPARD PPARG PPARGC1A PPP1R13B PPP1R13L PREB PROP1 PROX1 PRRX1 PTTG2 RARA RARG RAX RB1 RBL1 RBL2 RBPJ REL RELA RELB RFX1 RFX2 RFX3 RFX5 RFXANK RORA RORB RORC RREB1 RUNX1 RUNX2 RUVBL1 RXRA RXRB RXRB_HUMAN RXRG SFPQ SHOX SHOX2 SIM1 SIM2 SIX1 SIX2 SIX3 SIX4 SIX6 SKI SKIL SLC12A8 SLC2A4RG SMAD1 SMAD2 SMAD4 SMAD5 SMAD6 SMARCA2 SMARCA4 SMARCB1 SMARCC1 SNAI1 SNAI2 SNAPC1 SNAPC2 SNAPC3 SNW1 SOCS1 SOCS3 SOX1 SOX10 SOX11 SOX12 SOX14 SOX15 SOX17 SOX18 SOX2 SOX21 SOX3 SOX4 SOX5 SOX7 SOX8 SOX9 SP1 SP3 SP4 SPDEF SPI1 SPIB SREBF1 SREBF2 SRF SRY SS18 SS18L1 SSRP1 STAT1 STAT2 STAT3 STAT4 STAT5A STAT5B STAT6 STOX2 SUB1 SULT2A1 SUPT16H T TADA2L TADA3L TAF1 TAF10 TAF11 TAF12 TAF13 TAF1A TAF1C TAF4 TAF5 TAF6 TAF9 TAL1 TARBP2 TAZ TBP TBR1 TBX1 TBX18 TBX19 TBX2 TBX20 TBX21 TBX22 TBX3 TBX4 TBX5 TBX6 TCEB1 TCEB2 TCEB3 TCERG1 TCF12 TCF21 TCF3 TCF4 TCF7 TCF7L1 TEAD3 TEAD4 TEF TFAM TFAP2A TFAP2C TFAP4 TFCP2L1 TFDP1 TFEB TGIF1 TGIF2 THRA THRB TLE1 TLX1 TLX2 TLX3 TOPORS TP53 TP53BP1 TP63 TP73 TRIM24 TRIM33 TWIST1 UBP1 UBTF USF1 USF2 VAV1 VAX2 VDR VENTX VEZF1 VPS72 VSX2 WT1 XBP1 XRCC5 XRCC6 YWHAE YY1 ZBTB16 ZBTB17 ZBTB25 ZBTB33 ZBTB48 ZBTB6 ZBTB7A ZEB1 ZEB2 ZFHX3 ZFP37 ZFX ZFY ZHX1 ZIC1 ZIC2 ZKSCAN5 ZNF10 ZNF12 ZNF146 ZNF174 ZNF187 ZNF20 ZNF219 ZNF238 ZNF24 ZNF281 ZNF33A ZNF350 ZNF354A ZNF398 ZNF423 ZNF43 ZNF44 ZNF45 ZNF628 ZNF7 ZNF76 ZNF83 ZNF85