CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses (Q30887790)

18 September 2017

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses (English)

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18 September 2017

5

1 reference

18 September 2017

Vanja Haberle

1

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Piero Carninci

object named as

Piero Carninci

series ordinal

4

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Yoshihide Hayashizaki

series ordinal

3

object named as

Yoshihide Hayashizaki

1 reference

18 September 2017

2

Alistair R R Forrest

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PMC publication ID

4417143

18 September 2017

language of work or name

English

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publication date

4 February 2015

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18 September 2017

Nucleic Acids Research

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18 September 2017

43

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18 September 2017

8

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18 September 2017

e51

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Creative Commons Attribution 4.0 International

18 September 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

1 reference

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CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

21 June 2018

1 reference

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A promoter-level mammalian expression atlas

21 June 2018

1 reference

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An atlas of active enhancers across human cell types and tissues

21 June 2018

1 reference

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Two independent transcription initiation codes overlap on vertebrate core promoters

21 June 2018

1 reference

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JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

21 June 2018

1 reference

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Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

21 June 2018

1 reference

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Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

21 June 2018

1 reference

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Landscape of transcription in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

21 June 2018

1 reference

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Genome-wide analysis of promoter architecture in Drosophila melanogaster.

21 June 2018

1 reference

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Differential expression analysis for sequence count data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

The regulated retrotransposon transcriptome of mammalian cells

21 June 2018

1 reference

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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

21 June 2018

1 reference

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Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

A code for transcription initiation in mammalian genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Large-scale clustering of CAGE tag expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Dynamic usage of transcription start sites within core promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

A genomic code for nucleosome positioning

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Genome-wide analysis of mammalian promoter architecture and evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

The transcriptional landscape of the mammalian genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Tag-based approaches for transcriptome research and genome annotation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

The RNA polymerase II core promoter

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

Analysis of gene expression data using self-organizing maps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417143

21 June 2018

Identifiers

DOI

10.1093/NAR/GKV054

1 reference

18 September 2017

1 reference

PMC publication ID

4417143

18 September 2017

PubMed publication ID

25653163

1 reference

PMC publication ID

4417143