eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data (Q36194281)

12 August 2017

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data (English)

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James E Barrett

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Valentina Iotchkova

Valentina Iotchkova

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Jenny van Dongen

Jenny van Dongen

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Dirk S Paul

Dirk S Paul

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Guillaume Bourque

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Guillaume Bourque

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Willem H Ouwehand

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Reiner Siebert

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Sadia Saeed

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Hendrik Gerard Stunnenberg

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Hendrik G Stunnenberg

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Charles E Breeze

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12 August 2017

Lee M Butcher

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John C Ambrose

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Robert Lowe

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Vardhman K Rakyan

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Mattia Frontini

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Kate Downes

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Jonathan Laperle

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Pierre-Étienne Jacques

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Anke K Bergmann

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Edo Vellenga

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Filomena Matarese

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Joost H A Martens

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Andrew E Teschendorff

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Stephan Beck

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1 November 2016

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2137-2150

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describes a project that uses

12 August 2017

minfi

minfi

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.

1 reference

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Epigenome-wide Association Studies and the Interpretation of Disease -Omics

1 October 2017

1 reference

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An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies

1 October 2017

1 reference

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A quantitative epigenetic approach for the assessment of cigarette consumption

1 October 2017

1 reference

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Integrative analysis of 111 reference human epigenomes

1 October 2017

1 reference

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Normalization of CD4+ T cell metabolism reverses lupus

1 October 2017

1 reference

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The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.

1 October 2017

1 reference

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Function and information content of DNA methylation

1 October 2017

1 reference

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Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment.

1 October 2017

1 reference

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Genetic and epigenetic fine mapping of causal autoimmune disease variants

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Fine-tuning the central nervous system: microglial modelling of cells and synapses

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Advances in epigenome-wide association studies for common diseases

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Correcting for cell-type composition bias in epigenome-wide association studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Genome-wide DNA methylation patterns in naive CD4+ T cells from patients with primary Sjögren's syndrome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Marmal-aid--a database for Infinium HumanMethylation450

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Functional interpretation of non-coding sequence variation: concepts and challenges

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Recommendations for the design and analysis of epigenome-wide association studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Review of processing and analysis methods for DNA methylation array data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Protein tyrosine phosphatase receptor-like genes are frequently hypermethylated in sporadic colorectal cancer.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Systematic localization of common disease-associated variation in regulatory DNA

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

An integrated encyclopedia of DNA elements in the human genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

The T cell in Sjogren's syndrome: force majeure, not spectateur.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

DNA methylation arrays as surrogate measures of cell mixture distribution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Epigenome-wide association studies for common human diseases

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

A genome-wide DNA methylation study in colorectal carcinoma

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Breast cancer methylomes establish an epigenomic foundation for metastasis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

BEDTools: a flexible suite of utilities for comparing genomic features

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

An epigenetic signature in peripheral blood predicts active ovarian cancer

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Epigenetic stem cell signature in cancer

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

DNA methylation profiling of human chromosomes 6, 20 and 22

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

High-throughput localization of functional elements by quantitative chromatin profiling

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Accelerated generation of CD14+ monocyte-lineage cells from the bone marrow of rheumatoid arthritis patients

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Brave new epigenomes: the dawn of epigenetic engineering

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Epigenome-wide association studies without the need for cell-type composition

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

BLUEPRINT to decode the epigenetic signature written in blood.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

DNA-binding factors shape the mouse methylome at distal regulatory regions

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

High density DNA methylation array with single CpG site resolution

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5120369

Identification of a CpG island methylator phenotype in adrenocortical carcinomas

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27851974

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CELREP.2016.10.059

1 reference

release_zc3n4kivjzehxedk2r5wz2o2uu

12 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/zc3n4kivjzehxedk2r5wz2o2uu

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

12 August 2017

1 reference