Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data (Q33287630)

25 July 2017

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data (English)

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25 July 2017

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cis-regulatory element

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25 July 2017

Francesca Chiaromonte

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object named as

Francesca Chiaromonte

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25 July 2017

Ying Zhang

3

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Webb Miller

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object named as

Webb Miller

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25 July 2017

2

James Taylor

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25 July 2017

David C King

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25 July 2017

Yong Cheng

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25 July 2017

Heather A Lawson

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25 July 2017

Joel Martin

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25 July 2017

ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis

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25 July 2017

1 June 2007

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25 July 2017

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25 July 2017

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25 July 2017

775-786

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25 July 2017

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describes a project that uses

25 July 2017

ImageJ

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC1891337/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

1 reference

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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

21 June 2018

1 reference

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FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

21 June 2018

1 reference

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The ENCODE Project at UC Santa Cruz

21 June 2018

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ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

21 June 2018

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Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

21 June 2018

1 reference

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DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

21 June 2018

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A distal enhancer and an ultraconserved exon are derived from a novel retroposon

21 June 2018

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Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

21 June 2018

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The UCSC Genome Browser Database: update 2006

21 June 2018

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Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome

21 June 2018

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Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

21 June 2018

1 reference

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A haplotype map of the human genome

21 June 2018

1 reference

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

21 June 2018

1 reference

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Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

21 June 2018

1 reference

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Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

21 June 2018

1 reference

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Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3

21 June 2018

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Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment

21 June 2018

1 reference

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Dissociation of cohesin from chromosome arms and loss of arm cohesion during early mitosis depends on phosphorylation of SA2.

21 June 2018

1 reference

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Conserved non-genic sequences - an unexpected feature of mammalian genomes

21 June 2018

1 reference

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Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

21 June 2018

1 reference

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Evidence for widespread degradation of gene control regions in hominid genomes

21 June 2018

1 reference

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A model of the statistical power of comparative genome sequence analysis

21 June 2018

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Highly conserved non-coding sequences are associated with vertebrate development

21 June 2018

1 reference

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21 June 2018

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Active genes dynamically colocalize to shared sites of ongoing transcription

21 June 2018

1 reference

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Aligning multiple genomic sequences with the threaded blockset aligner

21 June 2018

1 reference

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Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome

21 June 2018

1 reference

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Scanning Human Gene Deserts for Long-Range Enhancers

21 June 2018

1 reference

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Association of genetic variation of the RIL gene, encoding a PDZ-LIM domain protein and localized in 5q31.1, with low bone mineral density in adult Japanese women

21 June 2018

1 reference

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Statistical significance for genomewide studies

21 June 2018

1 reference

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Human-mouse alignments with BLASTZ

21 June 2018

1 reference

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Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

21 June 2018

1 reference

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Cross-species sequence comparisons: a review of methods and available resources

21 June 2018

1 reference

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Looping and interaction between hypersensitive sites in the active beta-globin locus

21 June 2018

1 reference

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Initial sequencing and comparative analysis of the mouse genome

21 June 2018

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Long-range chromatin regulatory interactions in vivo

21 June 2018

1 reference

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Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover

21 June 2018

1 reference

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Capturing chromosome conformation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Genome-wide location and function of DNA binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Adaptive protein evolution at the Adh locus in Drosophila

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Adaptive evolution of non-coding DNA in Drosophila

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Megabase deletions of gene deserts result in viable mice

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

The share of human genomic DNA under selection estimated from human-mouse genomic alignments.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Significance of interspecies matches when evolutionary rate varies.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891337

31 October 2018

Identifiers

DOI

10.1101/GR.5592107

1 reference

25 July 2017

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25 July 2017

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