https://info.gersteinlab.org/index.php?action=history&feed=atom&title=Human_TF_List Human TF List - Revision history 2026-05-03T05:15:26Z Revision history for this page on the wiki MediaWiki 1.42.6 https://info.gersteinlab.org/index.php?title=Human_TF_List&diff=93&oldid=prev Infoadmin: Created page with ''''Here is the [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls list] with various gene names mapped.''' '''Citation:''' Bhardwaj, N., Carson, M. B., …' 2010-06-10T13:39:46Z <p>Created page with &#039;&#039;&#039;&#039;Here is the [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls list] with various gene names mapped.&#039;&#039;&#039; &#039;&#039;&#039;Citation:&#039;&#039;&#039; Bhardwaj, N., Carson, M. B., …&#039;</p> <p><b>New page</b></p><div>&#039;&#039;&#039;Here is the [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls list] with various gene names mapped.&#039;&#039;&#039;<br /> <br /> &#039;&#039;&#039;Citation:&#039;&#039;&#039; 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, &#039;&#039;PLoS Comp Biol&#039;&#039; (in press).<br /> <br /> <br /> &#039;&#039;&#039;Please read the following before using the file:&#039;&#039;&#039;<br /> <br /> &#039;&#039;&#039;Why are there more than one entries sometime for one TF?&#039;&#039;&#039;<br /> <br /> This list was compiled by cross-referencing various databases with other with BioMart as the main source.<br /> 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&#039;s there are many entries against one TF.<br /> Probably, the primary reason for this is that the multiple entries are splice-variants of the same TF. Hence, multiple entries.<br /> <br /> <br /> &#039;&#039;&#039;What does the first set of values indicate (Columns L through O)?&#039;&#039;&#039;<br /> <br /> These values are the normalized values obtained by normalizing (using Quantile Normalization) across different *REPLICATES* in the same cell line.<br /> <br /> <br /> &#039;&#039;&#039;Why are the values so different across different cell lines?&#039;&#039;&#039;<br /> <br /> 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.<br /> 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.<br /> Nonetheless, a simple z-score fashion normalization across these cell lines was performed(see below for the next set of normalized values).<br /> <br /> <br /> &#039;&#039;&#039;What do 1&#039;s and -&#039;s indicate (Columns P through S)?&#039;&#039;&#039;<br /> <br /> 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.<br /> <br /> <br /> <br /> &#039;&#039;&#039;What does the second set of values indicate (Columns T through W)?&#039;&#039;&#039;<br /> <br /> These values are obtained by further normalizing each TF across different cell lines in a Z-score fashion. <br /> New value = (old value - Mean of the entire data)/Std Deviation of the entire data<br /> <br /> <br /> &#039;&#039;&#039;How much can the Z-score fashion normalization be trusted?&#039;&#039;&#039;<br /> <br /> Not much. These values from different cell lines are coming from experiments done prossibly under drastically different conditions in diff labs.<br /> So, not sure how much sense does it make to do a z-score normalization.<br /> Moreover, Z-score works best when the data follows normal distribution. This one probably doesn&#039;t.<br /> <br /> <br /> <br /> &#039;&#039;&#039;Quick list of the TFs in Common name format.&#039;&#039;&#039; <br /> <br /> ABL1<br /> ACTL6A<br /> AFF3<br /> AHR<br /> AIRE<br /> ALX1<br /> ALX3<br /> ALX4<br /> APC<br /> APEX1<br /> AR<br /> ARID3A<br /> ARNT<br /> ARNT2<br /> ARNTL<br /> ARNTL2<br /> ATF1<br /> ATF2<br /> ATF3<br /> ATF4<br /> ATF5<br /> ATF6<br /> ATF7<br /> ATOH1<br /> BACH1<br /> BACH2<br /> BARHL2<br /> BCL3<br /> BCL6<br /> BHLHB2<br /> BHLHB3<br /> BIN1<br /> BNC1<br /> BRCA1<br /> BRCA2<br /> BRIP1<br /> BRPF1<br /> CBFB<br /> CCNH<br /> CCNT1<br /> CCNT2<br /> CDC2<br /> CDK2<br /> CDK7<br /> CDK9<br /> CDX1<br /> CDX2<br /> CDX4<br /> CEBPB<br /> CEBPD<br /> CEBPE<br /> CEBPG<br /> CEBPZ<br /> CIITA<br /> CLOCK<br /> CREB1<br /> CREB5<br /> CREBBP<br /> CRTC1<br /> CRTC2<br /> CRTC3<br /> CRX<br /> CSDA<br /> CTBP1<br /> CTCF<br /> CTNNB1<br /> CUTL1<br /> CUTL2<br /> DBP<br /> DDB1<br /> DDB2<br /> DDIT3<br /> DLX1<br /> DLX2<br /> DLX3<br /> DLX4<br /> DNMT1<br /> DR1<br /> E2F1<br /> E2F2<br /> E2F3<br /> E2F4<br /> E2F5<br /> EGR1<br /> EGR2<br /> EGR3<br /> EGR4<br /> ELF1<br /> ELF3<br /> ELF5<br /> ELK1<br /> ELK3<br /> ELK4<br /> EMX2<br /> EN1<br /> EN2<br /> EOMES<br /> EP300<br /> EPAS1<br /> ERCC2<br /> ERCC3<br /> ERCC8<br /> ERF<br /> ERG<br /> ESR1<br /> ESR2<br /> ESRRA<br /> ESRRB<br /> ESRRG<br /> ETS1<br /> ETS2<br /> ETV1<br /> ETV4<br /> ETV5<br /> ETV6<br /> ETV7<br /> EVI1<br /> EVX1<br /> EWSR1<br /> EZH1<br /> EZH2<br /> FEV<br /> FGF3<br /> FKHL18<br /> FLI1<br /> FOS<br /> FOSB<br /> FOSL1<br /> FOSL2<br /> FOXA1<br /> FOXA2<br /> FOXA3<br /> FOXB1<br /> FOXC1<br /> FOXC2<br /> FOXD2<br /> FOXD3<br /> FOXD4<br /> FOXE1<br /> FOXE3<br /> FOXF2<br /> FOXG1<br /> FOXH1<br /> FOXI1<br /> FOXJ1<br /> FOXJ2<br /> FOXJ3<br /> FOXK2<br /> FOXL1<br /> FOXL2<br /> FOXM1<br /> FOXN3<br /> FOXO1<br /> FOXO3<br /> FOXO4<br /> FOXP1<br /> FOXP2<br /> FOXP3<br /> FOXP4<br /> FOXQ1<br /> GABPA<br /> GABPB2<br /> GATA1<br /> GATA2<br /> GATA3<br /> GATA4<br /> GATA6<br /> GBX1<br /> GBX2<br /> GCN5L2<br /> GLI1<br /> GLI3<br /> GLIS2<br /> GMEB1<br /> GRHL1<br /> GSC<br /> GSCL<br /> GTF2A1<br /> GTF2A1L<br /> GTF2A2<br /> GTF2B<br /> GTF2E1<br /> GTF2E2<br /> GTF2F1<br /> GTF2F2<br /> GTF2H1<br /> GTF2H2<br /> GTF2H3<br /> GTF2I<br /> GZF1<br /> HAND1<br /> HDAC1<br /> HDAC2<br /> HDAC3<br /> HDAC4<br /> HDAC5<br /> HES1<br /> HES2<br /> HESX1<br /> HEY1<br /> HEY2<br /> HEYL<br /> HHEX<br /> HIC1<br /> HIF1A<br /> HIVEP2<br /> HLF<br /> HLX<br /> HMGA1<br /> HMGB1<br /> HMGB2<br /> HNF1A<br /> HNF1B<br /> HNF4A<br /> HNRNPA1<br /> HOXA1<br /> HOXA10<br /> HOXA11<br /> HOXA13<br /> HOXA2<br /> HOXA3<br /> HOXA4<br /> HOXA5<br /> HOXA6<br /> HOXA7<br /> HOXA9<br /> HOXB1<br /> HOXB13<br /> HOXB2<br /> HOXB3<br /> HOXB4<br /> HOXB5<br /> HOXB6<br /> HOXB7<br /> HOXB8<br /> HOXB9<br /> HOXC10<br /> HOXC11<br /> HOXC12<br /> HOXC13<br /> HOXC4<br /> HOXC5<br /> HOXC6<br /> HOXC8<br /> HOXC9<br /> HOXD10<br /> HOXD12<br /> HOXD3<br /> HOXD4<br /> HOXD8<br /> HOXD9<br /> HSBP1<br /> HSF1<br /> HSF2<br /> HSF4<br /> ID1<br /> ID2<br /> ID3<br /> IGFBP1<br /> IKZF1<br /> IKZF2<br /> IKZF3<br /> ING1<br /> INSM1<br /> IRF1<br /> IRF2<br /> IRF3<br /> IRF4<br /> IRF5<br /> IRF6<br /> IRF7<br /> IRF8<br /> IRF9<br /> IRX2<br /> IRX3<br /> IRX4<br /> IRX5<br /> IRX6<br /> JUN<br /> JUNB<br /> JUND<br /> KCNIP1<br /> KCNIP2<br /> KCNIP3<br /> KLF1<br /> KLF10<br /> KLF11<br /> KLF12<br /> KLF13<br /> KLF15<br /> KLF16<br /> KLF2<br /> KLF4<br /> KLF5<br /> KLF6<br /> KLF7<br /> KLF9<br /> LBX1<br /> LDB2<br /> LEF1<br /> LHX1<br /> LHX2<br /> LHX3<br /> LHX4<br /> LHX5<br /> LITAF<br /> LMO2<br /> LMO3<br /> LYL1<br /> MAF<br /> MAFA<br /> MAFB<br /> MAFF<br /> MAFG<br /> MAFK<br /> MAML1<br /> MAPK8IP1<br /> MAZ<br /> MECP2<br /> MED21<br /> MEF2A<br /> MEF2B<br /> MEF2C<br /> MEF2D<br /> MEIS1<br /> MEOX1<br /> MEOX2<br /> MIXL1<br /> MLL<br /> MLX<br /> MLXIP<br /> MLXIPL<br /> MNAT1<br /> MNT<br /> MNX1<br /> MSC<br /> MSX2<br /> MTA2<br /> MTF1<br /> MXD1<br /> MXI1<br /> MYB<br /> MYBBP1A<br /> MYBL1<br /> MYBL2<br /> MYC<br /> MYCBP<br /> MYCL1<br /> MYCN<br /> MYF5<br /> MYF6<br /> MYOCD<br /> MYOD1<br /> MYOG<br /> MYT1<br /> MZF1<br /> NAT10<br /> NCOA1<br /> NCOA2<br /> NCOA3<br /> NCOA6<br /> NCOR1<br /> NCOR2<br /> NEUROD1<br /> NEUROD2<br /> NEUROG1<br /> NEUROG3<br /> NF1<br /> NFAT5<br /> NFATC2<br /> NFATC3<br /> NFATC4<br /> NFE2<br /> NFE2L1<br /> NFE2L2<br /> NFE2L3<br /> NFIB<br /> NFKB2<br /> NFKBIA<br /> NFKBIB<br /> NFYA<br /> NFYB<br /> NHLH1<br /> NHLH2<br /> NKRF<br /> NKX2-1<br /> NKX2-2<br /> NKX2-5<br /> NKX2-8<br /> NKX3-1<br /> NKX3-2<br /> NKX6-1<br /> NKX6-2<br /> NME2<br /> NMI<br /> NONO<br /> NPAS1<br /> NPAS2<br /> NR0B1<br /> NR0B2<br /> NR1D1<br /> NR1D2<br /> NR1H2<br /> NR1H3<br /> NR1I2<br /> NR2E1<br /> NR2E3<br /> NR2F1<br /> NR2F2<br /> NR2F6<br /> NR3C1<br /> NR3C2<br /> NR4A1<br /> NR4A2<br /> NR4A3<br /> NR5A1<br /> NR5A2<br /> NR6A1<br /> NRF1<br /> NRL<br /> OLIG1<br /> OLIG2<br /> ONECUT1<br /> ONECUT2<br /> OTX1<br /> OTX2<br /> PAX1<br /> PAX2<br /> PAX3<br /> PAX5<br /> PAX6<br /> PAX7<br /> PAX8<br /> PAX9<br /> PBX1<br /> PBX2<br /> PBX2_HUMAN<br /> PBX3<br /> PCAF<br /> PCGF2<br /> PDX1<br /> PFDN5<br /> PGBD3<br /> PGR<br /> PHOX2A<br /> PHOX2B<br /> PITX1<br /> PITX2<br /> PITX3<br /> PKNOX1<br /> PKNOX2<br /> PLAGL1<br /> PLAGL2<br /> PML<br /> PO5F1_HUMAN<br /> POU1F1<br /> POU2AF1<br /> POU2F1<br /> POU2F3<br /> POU3F1<br /> POU3F2<br /> POU3F3<br /> POU3F4<br /> POU4F1<br /> POU4F3<br /> POU5F1<br /> POU6F1<br /> PPARA<br /> PPARD<br /> PPARG<br /> PPARGC1A<br /> PPP1R13B<br /> PPP1R13L<br /> PREB<br /> PROP1<br /> PROX1<br /> PRRX1<br /> PTTG2<br /> RARA<br /> RARG<br /> RAX<br /> RB1<br /> RBL1<br /> RBL2<br /> RBPJ<br /> REL<br /> RELA<br /> RELB<br /> RFX1<br /> RFX2<br /> RFX3<br /> RFX5<br /> RFXANK<br /> RORA<br /> RORB<br /> RORC<br /> RREB1<br /> RUNX1<br /> RUNX2<br /> RUVBL1<br /> RXRA<br /> RXRB<br /> RXRB_HUMAN<br /> RXRG<br /> SFPQ<br /> SHOX<br /> SHOX2<br /> SIM1<br /> SIM2<br /> SIX1<br /> SIX2<br /> SIX3<br /> SIX4<br /> SIX6<br /> SKI<br /> SKIL<br /> SLC12A8<br /> SLC2A4RG<br /> SMAD1<br /> SMAD2<br /> SMAD4<br /> SMAD5<br /> SMAD6<br /> SMARCA2<br /> SMARCA4<br /> SMARCB1<br /> SMARCC1<br /> SNAI1<br /> SNAI2<br /> SNAPC1<br /> SNAPC2<br /> SNAPC3<br /> SNW1<br /> SOCS1<br /> SOCS3<br /> SOX1<br /> SOX10<br /> SOX11<br /> SOX12<br /> SOX14<br /> SOX15<br /> SOX17<br /> SOX18<br /> SOX2<br /> SOX21<br /> SOX3<br /> SOX4<br /> SOX5<br /> SOX7<br /> SOX8<br /> SOX9<br /> SP1<br /> SP3<br /> SP4<br /> SPDEF<br /> SPI1<br /> SPIB<br /> SREBF1<br /> SREBF2<br /> SRF<br /> SRY<br /> SS18<br /> SS18L1<br /> SSRP1<br /> STAT1<br /> STAT2<br /> STAT3<br /> STAT4<br /> STAT5A<br /> STAT5B<br /> STAT6<br /> STOX2<br /> SUB1<br /> SULT2A1<br /> SUPT16H<br /> T<br /> TADA2L<br /> TADA3L<br /> TAF1<br /> TAF10<br /> TAF11<br /> TAF12<br /> TAF13<br /> TAF1A<br /> TAF1C<br /> TAF4<br /> TAF5<br /> TAF6<br /> TAF9<br /> TAL1<br /> TARBP2<br /> TAZ<br /> TBP<br /> TBR1<br /> TBX1<br /> TBX18<br /> TBX19<br /> TBX2<br /> TBX20<br /> TBX21<br /> TBX22<br /> TBX3<br /> TBX4<br /> TBX5<br /> TBX6<br /> TCEB1<br /> TCEB2<br /> TCEB3<br /> TCERG1<br /> TCF12<br /> TCF21<br /> TCF3<br /> TCF4<br /> TCF7<br /> TCF7L1<br /> TEAD3<br /> TEAD4<br /> TEF<br /> TFAM<br /> TFAP2A<br /> TFAP2C<br /> TFAP4<br /> TFCP2L1<br /> TFDP1<br /> TFEB<br /> TGIF1<br /> TGIF2<br /> THRA<br /> THRB<br /> TLE1<br /> TLX1<br /> TLX2<br /> TLX3<br /> TOPORS<br /> TP53<br /> TP53BP1<br /> TP63<br /> TP73<br /> TRIM24<br /> TRIM33<br /> TWIST1<br /> UBP1<br /> UBTF<br /> USF1<br /> USF2<br /> VAV1<br /> VAX2<br /> VDR<br /> VENTX<br /> VEZF1<br /> VPS72<br /> VSX2<br /> WT1<br /> XBP1<br /> XRCC5<br /> XRCC6<br /> YWHAE<br /> YY1<br /> ZBTB16<br /> ZBTB17<br /> ZBTB25<br /> ZBTB33<br /> ZBTB48<br /> ZBTB6<br /> ZBTB7A<br /> ZEB1<br /> ZEB2<br /> ZFHX3<br /> ZFP37<br /> ZFX<br /> ZFY<br /> ZHX1<br /> ZIC1<br /> ZIC2<br /> ZKSCAN5<br /> ZNF10<br /> ZNF12<br /> ZNF146<br /> ZNF174<br /> ZNF187<br /> ZNF20<br /> ZNF219<br /> ZNF238<br /> ZNF24<br /> ZNF281<br /> ZNF33A<br /> ZNF350<br /> ZNF354A<br /> ZNF398<br /> ZNF423<br /> ZNF43<br /> ZNF44<br /> ZNF45<br /> ZNF628<br /> ZNF7<br /> ZNF76<br /> ZNF83<br /> ZNF85</div> Infoadmin