Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines

scientific article

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1186/1471-2164-14-720
P932PMC publication ID3826616
P698PubMed publication ID24138567
P5875ResearchGate publication ID258057942

P50authorJoseph W FoleyQ46974657
P2093author name stringArend Sidow
P2860cites workClassification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factorsQ21183997
Differential expression analysis for sequence count dataQ21184103
Interaction between the two ubiquitously expressed transcription factors NF-Y and Sp1Q22010213
An integrated encyclopedia of DNA elements in the human genomeQ22122150
Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with MycQ24294647
MTA3 and the Mi-2/NuRD complex regulate cell fate during B lymphocyte differentiationQ24305562
REST: A mammalian silencer protein that restricts sodium channel gene expression to neuronsQ24312038
BCL3 encodes a nuclear protein which can alter the subcellular location of NF-kappa B proteinsQ24315909
Molecular characterization of the novel basic helix-loop-helix protein DEC1 expressed in differentiated human embryo chondrocytesQ24319890
Mxi1, a protein that specifically interacts with Max to bind Myc-Max recognition sitesQ24320277
HEB, a Helix-Loop-Helix Protein Related to E2A and ITF2 That Can Modulate the DNA-Binding Ability of Myogenic Regulatory FactorsQ24328835
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promotersQ24537436
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq dataQ24595121
Histone H3K27ac separates active from poised enhancers and predicts developmental stateQ24628758
An atlas of combinatorial transcriptional regulation in mouse and manQ24630300
Regulation of the cfos serum response element by C/EBPbetaQ24647062
Fast and accurate short read alignment with Burrows-Wheeler transformQ24653853
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promotersQ24674136
The neighbor-joining method: a new method for reconstructing phylogenetic treesQ25939010
Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcriptionQ28131686
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeQ28131828
Ras regulates the association of serum response factor and CCAAT/enhancer-binding protein betaQ28143523
Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesisQ28201509
Members of the USF family of helix-loop-helix proteins bind DNA as homo- as well as heterodimersQ28204750
Mad-Max transcriptional repression is mediated by ternary complex formation with mammalian homologs of yeast repressor Sin3Q28236241
E2A proteins are required for proper B cell development and initiation of immunoglobulin gene rearrangementsQ28243194
Regulation of transcription by dimerization of erythroid factor NF-E2 p45 with small Maf proteinsQ28249579
A transcription factor collective defines cardiac cell fate and reflects lineage historyQ28258920
Combining evidence using p-values: application to sequence homology searchesQ28265811
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectQ28301622
Co-evolution from yeast to mouse: cDNA cloning of the two NF-Y (CP-1/CBF) subunitsQ28506331
Bcl11a is essential for normal lymphoid developmentQ28511014
Transcription factor Mef2c is required for B cell proliferation and survival after antigen receptor stimulationQ28586846
Role of PML in cell growth and the retinoic acid pathwayQ28593138
The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cellsQ28593666
Genome-wide mapping of in vivo protein-DNA interactionsQ29547162
Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activityQ29555842
A unique chromatin signature uncovers early developmental enhancers in humansQ29614327
Genome-wide analysis of mammalian promoter architecture and evolutionQ29616717
Architecture of the human regulatory network derived from ENCODE dataQ29617046
Identification of functional elements and regulatory circuits by Drosophila modENCODEQ29617551
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policyQ29617901
Cohesin mediates transcriptional insulation by CCCTC-binding factorQ29618130
A census of human transcription factors: function, expression and evolutionQ29622841
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.Q30562517
Identifying a high fraction of the human genome to be under selective constraint using GERP++.Q33769754
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencingQ33889403
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiationQ34058172
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolutionQ34239260
Characterization of myocyte enhancer factor 2 (MEF2) expression in B and T cells: MEF2C is a B cell-restricted transcription factor in lymphocytes.Q34478174
Hotspots of transcription factor colocalization in the genome of Drosophila melanogasterQ35033165
Runx3 and Runx1 are required for CD8 T cell development during thymopoiesisQ35146679
A cis-regulatory map of the Drosophila genome.Q35229726
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cellsQ35672244
Targeted disruption of the PU.1 gene results in multiple hematopoietic abnormalitiesQ35911056
A novel lineage-specific nuclear factor regulates mb-1 gene transcription at the early stages of B cell differentiationQ35933722
B-lymphocyte development is regulated by the combined dosage of three basic helix-loop-helix genes, E2A, E2-2, and HEB.Q36560174
Pax5: the guardian of B cell identity and functionQ36794303
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regionsQ37309445
Identification of potential target genes for the neuron-restrictive silencer factorQ37366344
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cellsQ37463190
A yeast and a human CCAAT-binding protein have heterologous subunits that are functionally interchangeableQ38347507
Late induction of CREB/ATF binding and a concomitant increase in cAMP levels in T and B lymphocytes stimulated via the antigen receptorQ38356557
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factorsQ39283917
JunD regulates lymphocyte proliferation and T helper cell cytokine expressionQ40735771
STAT5 interaction with the T cell receptor complex and stimulation of T cell proliferation.Q40982703
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signatureQ41766976
Clast5/Stra13 is a negative regulator of B lymphocyte activationQ42817669
Disruption of Rxra gene in thymocytes and T lymphocytes modestly alters lymphocyte frequencies, proliferation, survival and T helper type 1/type 2 balanceQ46788449
Oct-2 is required early in T cell-independent B cell activation for G1 progression and for proliferationQ51130519
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.Q51827112
Essential role for Bclaf1 in lung development and immune system function.Q51946594
Transcription factor IRF4 controls plasma cell differentiation and class-switch recombination.Q51981842
REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis.Q52049234
Stat3 activation is responsible for IL-6-dependent T cell proliferation through preventing apoptosis: generation and characterization of T cell-specific Stat3-deficient mice.Q52182764
NFATc1 and NFATc2 together control both T and B cell activation and differentiationQ73406639
P4510describes a project that usesDESeq2Q113018293
P407language of work or nameEnglishQ1860
P304page(s)720
P577publication date2013-10-20
P1433published inBMC GenomicsQ15765854
P1476titleTranscription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines
P478volume14

Reverse relations

cites work (P2860)
Q38303263A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.
Q34626036Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
Q31159938Copy number variation is a fundamental aspect of the placental genome.
Q35896285Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus
Q35097079Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation
Q26825151From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks
Q35784256Functional annotation of HOT regions in the human genome: implications for human disease and cancer.
Q36134892Genome-wide identification and characterisation of HOT regions in the human genome.
Q46974573HEB associates with PRC2 and SMAD2/3 to regulate developmental fates
Q96953978IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity
Q35130969Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
Q53057180JMJD5 regulates cell cycle and pluripotency in human embryonic stem cells.
Q58722010KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons
Q35535448Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Q41221853Molecular conservation of marsupial and eutherian placentation and lactation
Q38882157RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Q43003988Spurious transcription factor binding: non-functional or genetically redundant?
Q55256745Theoretical principles of transcription factor traffic on folded chromatin.
Q58597717Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites

Search more.