Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. (Q38341537)

2 September 2017

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. (English)

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2 September 2017

2

1 reference

2 September 2017

Morana Vitezic

1

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Carsten O Daub

object named as

Carsten O Daub

series ordinal

10

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Piero Carninci

object named as

Piero Carninci

series ordinal

7

0 references

Yoshihide Hayashizaki

series ordinal

9

object named as

Yoshihide Hayashizaki

1 reference

2 September 2017

8

Harukazu Suzuki

1 reference

2 September 2017

3

Alistair R R Forrest

1 reference

2 September 2017

5

Yasuhiro Tomaru

1 reference

2 September 2017

4

Masanori Suzuki

1 reference

2 September 2017

Jun Kawai

6

1 reference

PMCID

3001087

2 September 2017

language of work or name

English

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publication date

19 August 2010

1 reference

2 September 2017

Nucleic Acids Research

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2 September 2017

38

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2 September 2017

22

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2 September 2017

8141-8148

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Creative Commons Attribution-NonCommercial 2.5 Generic

2 September 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

ChIP on chip assays: genome-wide analysis of transcription factor binding and histone modifications

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

6 September 2017

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TFCat: the curated catalog of mouse and human transcription factors

6 September 2017

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

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

6 September 2017

1 reference

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Extracting biology from high-dimensional biological data

6 September 2017

1 reference

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Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters

6 September 2017

1 reference

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MEME: discovering and analyzing DNA and protein sequence motifs

6 September 2017

1 reference

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Genome-wide analysis of mammalian promoter architecture and evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

GENE SEQUENCING: The Race for the $1000 Genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

CAGE: cap analysis of gene expression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

The transcriptional landscape of the mammalian genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Genomic studies of transcription factor-DNA interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Applied bioinformatics for the identification of regulatory elements

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Detection of functional DNA motifs via statistical over-representation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Cytoscape: a software environment for integrated models of biomolecular interaction networks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

MATCH: A tool for searching transcription factor binding sites in DNA sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

IFN-stimulated gene 15 is synergistically activated through interactions between the myelocyte/lymphocyte-specific transcription factors, PU.1, IFN regulatory factor-8/IFN consensus sequence binding protein, and IFN regulatory factor-4: characteriza

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

PU.1/Interferon Regulatory Factor interactions: mechanisms of transcriptional regulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Initial sequencing and analysis of the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Establishment and characterization of a human acute monocytic leukemia cell line (THP-1)

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

New light on Myc and Myb. Part II. Myb.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Meta-MEME: motif-based hidden Markov models of protein families

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

Transcriptional regulation of CHI3L1, a marker gene for late stages of macrophage differentiation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3001087

31 August 2018

Identifiers

DOI

10.1093/NAR/GKQ729

1 reference

2 September 2017

1 reference

2 September 2017

1 reference

PMCID

3001087