Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs

scientific article published on 30 December 2014

Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/bmcbi/Joshi14
P6179Dimensions Publication ID1014642176
P356DOI10.1186/S12859-014-0412-0
P2888exact matchhttps://scigraph.springernature.com/pub.10.1186/s12859-014-0412-0
P8608Fatcat IDrelease_qeulh5s3hvc3xkpiu2c2uone44
P932PMC publication ID4302108
P698PubMed publication ID25547756
P5875ResearchGate publication ID270291668

P2093author name stringAnagha Joshi
P2860cites workA user's guide to the encyclopedia of DNA elements (ENCODE)Q21092716
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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identitiesQ24617969
Histone H3K27ac separates active from poised enhancers and predicts developmental stateQ24628758
Negative and positive regulation of gene expression by mouse histone deacetylase 1Q24672508
VISTA Enhancer Browser--a database of tissue-specific human enhancersQ24676452
Genome-wide nucleosome positioning during embryonic stem cell developmentQ28277658
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Oct4 and LIF/Stat3 additively induce Krüppel factors to sustain embryonic stem cell self-renewal.Q51921401
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factorsQ28506983
ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250aQ28508327
Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional networkQ28513471
Esrrb is a pivotal target of the Gsk3/Tcf3 axis regulating embryonic stem cell self-renewalQ28910178
Integration of external signaling pathways with the core transcriptional network in embryonic stem cellsQ29547179
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cellsQ29615089
In vivo enhancer analysis of human conserved non-coding sequencesQ29616554
Identification of functional elements and regulatory circuits by Drosophila modENCODEQ29617551
Master transcription factors and mediator establish super-enhancers at key cell identity genesQ29618062
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding dataQ30580583
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data.Q31157497
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seqMINER: an integrated ChIP-seq data interpretation platformQ33777909
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liverQ34018312
Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read dataQ34185764
Dnmt3a is essential for hematopoietic stem cell differentiationQ34237926
Mouse duplicate genes are as essential as singletonsQ34636141
Extensive low-affinity transcriptional interactions in the yeast genomeQ34881942
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell linesQ35020492
Hotspots of transcription factor colocalization in the genome of Drosophila melanogasterQ35033165
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in DrosophilaQ36504410
Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and NanogQ36833192
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regionsQ37309445
Transcriptional networks and chromatin remodeling controlling adipogenesisQ37955512
Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators.Q39649034
Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci.Q40497945
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signatureQ41766976
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammalsQ42020759
HOT DNAs: a novel class of developmental enhancersQ42085279
DNA-binding factors shape the mouse methylome at distal regulatory regionsQ42818364
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCsQ42826399
A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanismsQ44891300
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P304page(s)412
P577publication date2014-12-30
P1433published inBMC BioinformaticsQ4835939
P1476titleMammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
P478volume15

Reverse relations

cites work (P2860)
Q36160675Cell type-selective disease-association of genes under high regulatory load
Q91973465Computational Biology Solutions to Identify Enhancers-target Gene Pairs
Q59330161Insights into mammalian transcription control by systematic analysis of ChIP sequencing data
Q36896396Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine.
Q34490684Transcription factor co-occupied regions in the murine genome constitute T-helper-cell subtype-specific enhancers.

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