High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells - Wikidata - awgldk - TriplyDB

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

http://www.wikidata.org/entity/Q24614543

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A user's guide to the encyclopedia of DNA elements (ENCODE)Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data An integrated encyclopedia of DNA elements in the human genome Epigenetic priors for identifying active transcription factor binding sites Pioneer transcription factors: establishing competence for gene expression Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome Transcriptional Enhancers in the Regulation of T Cell Differentiation Identifying novel transcriptional components controlling energy metabolism HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.Protein-DNA binding in high-resolution CTCF Recruits Centromeric Protein CENP-E to the Pericentromeric/Centromeric Regions of Chromosomes through Unusual CTCF-Binding Sites Lagging-strand replication shapes the mutational landscape of the genome Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages Annotation of functional variation in personal genomes using RegulomeDB EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies.Using DNase digestion data to accurately identify transcription factor binding sites Chromatin associations in Arabidopsis interphase nuclei Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium.The RUNX2 cistrome in osteoblasts: characterization, down-regulation following differentiation, and relationship to gene expression.NicE-seq: high resolution open chromatin profiling.DREME: motif discovery in transcription factor ChIP-seq data.Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.Technical considerations for functional sequencing assays.Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations.Site-specific chromatin immunoprecipitation: a selective method to individually analyze neighboring transcription factor binding sites in vivo.Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.Accurate prediction of inducible transcription factor binding intensities in vivo.Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Linking disease associations with regulatory information in the human genome.CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization.

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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

http://www.wikidata.org/entity/Q24614543

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2011 nî lūn-bûn

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2011 թուականի Մարտին հրատարակուած գիտական յօդուած

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Genome Research

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Bum-Kyu Lee

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Lingyun Song

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Vishwanath R Iyer

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P2860

An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

CTCF: master weaver of the genome

An atlas of combinatorial transcriptional regulation in mouse and man

DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

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10.1101/GR.112656.110

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21

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Terrence S. Furey

Gregory E Crawford

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49635133

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21106903

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3044859

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