Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (Q39632067)

13 September 2017

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (English)

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13 September 2017

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13 September 2017

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13 September 2017

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13 September 2017

Carsten O Daub

12

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Piero Carninci

object named as

Piero Carninci

series ordinal

10

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Yoshihide Hayashizaki

series ordinal

11

object named as

Yoshihide Hayashizaki

1 reference

13 September 2017

Katharine Irvine

8

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Marina Lizio

series ordinal

3

object named as

Marina Lizio

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13 September 2017

9

Harukazu Suzuki

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13 September 2017

2

Jessica Severin

1 reference

13 September 2017

6

Michael Rehli

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13 September 2017

4

Alistair R R Forrest

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PMCID

3013704

13 September 2017

language of work or name

English

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publication date

12 November 2010

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13 September 2017

Nucleic Acids Research

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13 September 2017

39

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13 September 2017

Database issue

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13 September 2017

D856-60

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Creative Commons Attribution-NonCommercial 2.5 Generic

13 September 2017

start time

14 November 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

The RIKEN integrated database of mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

An atlas of combinatorial transcriptional regulation in mouse and man

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

ENCODE whole-genome data in the UCSC Genome Browser

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

MirZ: an integrated microRNA expression atlas and target prediction resource

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The regulated retrotransposon transcriptome of mammalian cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Data-driven normalization strategies for high-throughput quantitative RT-PCR.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Inference of miRNA targets using evolutionary conservation and pathway analysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Genome-wide analysis of mammalian promoter architecture and evolution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Antisense transcription in the mammalian transcriptome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The transcriptional landscape of the mammalian genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Tag-based approaches for transcriptome research and genome annotation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The generic genome browser: a building block for a model organism system database

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Functional annotation of a full-length mouse cDNA collection

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

SwissRegulon: a database of genome-wide annotations of regulatory sites

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

Tiny RNAs associated with transcription start sites in animals.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013704

21 August 2018

Identifiers

DOI

10.1093/NAR/GKQ1112

1 reference

journals/nar/KawajiSLFNRSISCHD11

13 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

13 September 2017

1 reference

PMCID

3013704