标题
Characterization of Enhancer Function from Genome-Wide Analyses
作者
关键词
-
出版物
Annual Review of Genomics and Human Genetics
Volume 13, Issue 1, Pages 29-57
出版商
Annual Reviews
发表日期
2012-06-16
DOI
10.1146/annurev-genom-090711-163723
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
- (2012) Guoliang Li et al. CELL
- A decade of 3C technologies: insights into nuclear organization
- (2012) E. de Wit et al. GENES & DEVELOPMENT
- HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter
- (2012) M. Visser et al. GENOME RESEARCH
- Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules
- (2011) Marc S Halfon et al. BMC GENOMICS
- Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling
- (2011) Alan C. Mullen et al. CELL
- Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells
- (2011) Oren Ram et al. CELL
- Animal Transcription Networks as Highly Connected, Quantitative Continua
- (2011) Mark D. Biggin DEVELOPMENTAL CELL
- Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators
- (2011) Marloes R. Tijssen et al. DEVELOPMENTAL CELL
- Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development
- (2011) Ralph Stadhouders et al. EMBO JOURNAL
- H3K4 tri-methylation provides an epigenetic signature of active enhancers
- (2011) Aleksandra Pekowska et al. EMBO JOURNAL
- Pioneer transcription factors: establishing competence for gene expression
- (2011) K. S. Zaret et al. GENES & DEVELOPMENT
- Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin
- (2011) D. G. Ceschin et al. GENES & DEVELOPMENT
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- (2011) D. S. Castro et al. GENES & DEVELOPMENT
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- (2011) Y. Lustig et al. GENES & DEVELOPMENT
- Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
- (2011) I. M. Min et al. GENES & DEVELOPMENT
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- (2011) M. Bergsland et al. GENES & DEVELOPMENT
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- (2011) A. Ozdemir et al. GENOME RESEARCH
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- (2011) I. Ioshikhes et al. GENOME RESEARCH
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- (2011) Hong-Bing Yu et al. GENOME RESEARCH
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- (2011) A. A. Serandour et al. GENOME RESEARCH
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- (2011) Gabriel E. Zentner et al. GENOME RESEARCH
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- (2011) S. De et al. MOLECULAR AND CELLULAR BIOLOGY
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- (2011) Arnaud R. Krebs et al. MOLECULAR CELL
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- (2011) Anton Valouev et al. NATURE
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- (2011) Dong Wang et al. NATURE
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- (2010) V. Gotea et al. GENOME RESEARCH
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- (2010) M. R. Tallack et al. GENOME RESEARCH
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- (2010) T. Mondal et al. GENOME RESEARCH
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- (2010) A. P. Boyle et al. GENOME RESEARCH
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- (2010) L. Laurent et al. GENOME RESEARCH
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- (2010) Lian Li et al. HUMAN MOLECULAR GENETICS
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- (2010) Serena Ghisletti et al. IMMUNITY
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- (2010) Sven Heinz et al. MOLECULAR CELL
- Integrative model of genomic factors for determining binding site selection by estrogen receptor-α
- (2010) Roy Joseph et al. Molecular Systems Biology
- Comprehensive methylome map of lineage commitment from haematopoietic progenitors
- (2010) Hong Ji et al. NATURE
- Phenotypic robustness conferred by apparently redundant transcriptional enhancers
- (2010) Nicolás Frankel et al. NATURE
- Widespread transcription at neuronal activity-regulated enhancers
- (2010) Tae-Kyung Kim et al. NATURE
- A unique chromatin signature uncovers early developmental enhancers in humans
- (2010) Alvaro Rada-Iglesias et al. NATURE
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- (2010) Rajnish A. Gupta et al. NATURE
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- (2010) Michael H. Kagey et al. NATURE
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- (2010) Housheng Hansen He et al. NATURE GENETICS
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- (2010) Galih Kunarso et al. NATURE GENETICS
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- (2010) Yin C Lin et al. NATURE IMMUNOLOGY
- Inducible gene expression: diverse regulatory mechanisms
- (2010) Vikki M. Weake et al. NATURE REVIEWS GENETICS
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- (2010) NATURE REVIEWS MOLECULAR CELL BIOLOGY
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- (2010) Thea A Egelhofer et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
- (2010) E. Y. Lee et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Histone H3K27ac separates active from poised enhancers and predicts developmental state
- (2010) M. P. Creyghton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
- (2010) D. Schmidt et al. SCIENCE
- Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans
- (2010) R. McDaniell et al. SCIENCE
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- (2010) Francesca De Santa et al. PLOS BIOLOGY
- Assessing Computational Methods of Cis-Regulatory Module Prediction
- (2010) Jing Su et al. PLoS Computational Biology
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- (2010) Michael P. Schnetz et al. PLoS Genetics
- Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes
- (2009) Zhibin Wang et al. CELL
- Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation
- (2009) Kairong Cui et al. Cell Stem Cell
- Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse
- (2009) Miriam R. Kantorovitz et al. DEVELOPMENTAL CELL
- ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands
- (2009) Willem-Jan Welboren et al. EMBO JOURNAL
- Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells
- (2009) J. Xu et al. GENES & DEVELOPMENT
- Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells
- (2009) P. Yuan et al. GENES & DEVELOPMENT
- Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
- (2009) A. W. Bruce et al. GENOME RESEARCH
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- (2009) T. E. Reddy et al. GENOME RESEARCH
- Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- (2009) Y. Cheng et al. GENOME RESEARCH
- Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery
- (2009) J. Boros et al. GENOME RESEARCH
- Histone modifications at human enhancers reflect global cell-type-specific gene expression
- (2009) Nathaniel D. Heintzman et al. NATURE
- An oestrogen-receptor-α-bound human chromatin interactome
- (2009) Melissa J. Fullwood et al. NATURE
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- (2009) Ryan Lister et al. NATURE
- ChIP-seq accurately predicts tissue-specific activity of enhancers
- (2009) Axel Visel et al. NATURE
- Defining mechanisms that regulate RNA polymerase II transcription in vivo
- (2009) Nicholas J. Fuda et al. NATURE
- H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
- (2009) Chunyuan Jin et al. NATURE GENETICS
- Sequencing technologies — the next generation
- (2009) Michael L. Metzker NATURE REVIEWS GENETICS
- Insights from genomic profiling of transcription factors
- (2009) Peggy J. Farnham NATURE REVIEWS GENETICS
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- Developmental programming of CpG island methylation profiles in the human genome
- (2009) Ravid Straussman et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Mapping accessible chromatin regions using Sono-Seq
- (2009) R. K. Auerbach et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
- (2009) Ahmad M. Khalil et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2009) Z. Ouyang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2009) E. Lieberman-Aiden et al. SCIENCE
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- (2008) G. Mittler et al. GENOME RESEARCH
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- (2008) Xiaodong Zhang et al. NATURE METHODS
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- (2008) J.-S. Kim et al. NUCLEIC ACIDS RESEARCH
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- (2008) Xiao-yong Li et al. PLOS BIOLOGY
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