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The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome sequence. These elements include genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, hypersensitive to cleavage of DNase I, etc. We organize the on-going analysis results of TF binding data in the web accessible repository factorbook.org.

Chromatin Immunoprecipitation (ChIP-seq) is the experimental technique used to generate TF-binding data, and the genomic regions bound by TFs are called ChIP-seq peaks. The transcription factor binding sites (TFBS) are the positions on the genomic DNA bound by TFs and tend to be located around the summits of ChIP-seq peaks. Below is a matrix of all ENCODE TF ChIP-seq datasets, arranged by cell lines. Click the TF name of interest to access individual pages.

Protein FamilyAllAcyl-CoA N-acyltransferases (Nat)Ankyrin repeatArginase/deacetylasebeta and beta-prime subunits of DNA dependent RNA-polymerasebeta-beta-alpha zinc fingersBRK domain-likeChromo domain-likeCyclin-likeDHS-like NAD/FAD-binding domainDNA-binding domainE set domainsFormate/glycerate dehydrogenase catalytic domain-likeFYVE/PHD zinc fingerGlucocorticoid receptor-like (DNA-binding domain)Histone-foldHLH, helix-loop-helix DNA-binding domainHomeodomain-likeLeucine zipper domainP-loop containing nucleoside triphosphate hydrolasesp53-like transcription factorsPAH2 domainRNA-binding domain, RBDSmc hinge domainSRF-likeTAF(II)230 TBP-binding fragmentTATA-box binding protein-likeTAZ domainUnknownWD40 repeat-likeWinged helix DNA-binding domainXRCC4, N-terminal domain
Type              AllATP-dependent chromatin complexesCyclin Kinase associated with transcriptionDNA repairgeneral Pol II associated factor, not site-specifichistone acetylation complexeshistone deacetylation complexeshistone methylation complexesPol II co-repressor/co-activatorPol II subunitPol II TFPol III associated

Cellline» «Factor

A549 AG04449 AG04450 AG09309 AG09319 AG10803 AoAF BE2_C BJ Caco-2 ECC-1 FetalPBDE GM06990 GM10847 GM12864 GM12865 GM12872 GM12873 GM12874 GM12875 GM12878 GM12891 GM12892 GM15510 GM18505 GM18526 GM18951 GM19099 GM19193 H1-hESC HA-sp HAc HBMEC HCFaa HCM HCPEpiC HCT-116 HEEpiC HEK293 HeLa-S3 HepG2 HFF-Myc HMEC HMF HPAF HPF HRE HRPEpiC HSMM HSMMtube HUVEC K562 MCF-7 MCF10A-Er-Src NB4 NH-A NHDF-Ad NHEK NHLF NT2-D1 Osteobl PANC-1 PBDE PFSK-1 Raji SAEC SH-SY5Y SK-N-MC SK-N-SH SK-N-SH_RA T-47D T-REx-HEK293 U2OS U87 WERI-Rb-1 WI-38

AP-2alpha AP-2gamma ATF3 BAF155 BAF170 BATF BCL11A BCL3 BCLAF1 BDP1 BHLHE40 BRCA1 BRF1 BRF2 BRG1 c-Fos c-Jun c-Myc CCNT2 CEBPB CHD2 CtBP2 CTCF CTCFL E2F1 E2F4 E2F6 EBF1 EGR-1 ELF1 ELK4 ERalpha a ERRA ETS1 FOSL1 FOSL2 FOXA1 FOXA2 FOXP2 GABP GATA1 GATA2 GATA3 GR GTF2B GTF2F1 HDAC2 HDAC8 HMGN3 HNF4A HNF4G HSF1 INI1 IRF1 IRF3 JunB JunD KAP1 MAFF MAFK MAX MEF2A MEF2C MXI1 NANOG NELFe NF-E2 NF-YA NF-YB NFKB NRF1 NRSF p300 PAX5 PBX3 PGC1A POL2 POL3 POU2F2 POU5F1 PRDM1 PU.1 RAD21 RFX5 RPC155 RXRA SETDB1 SIN3A SIRT6 SIX5 SMC3 SP1 SP2 SREBP1 SRF STAT1 STAT2 STAT3 SUZ12 TAF1 TAF7 TAL1 TBP TCF12 TCF7L2 TFIIIC-110 THAP1 TR4 USF1 USF2 WHIP YY1 ZBTB33 ZBTB7A ZEB1 ZNF143 ZNF263 ZNF274 ZZZ3

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