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Roadmap Epigenomics Project specifications

Information


Unique identifier OMICS_19328
Name Roadmap Epigenomics Project
Alternative name Roadmap Epigenomics
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Roadmap Epigenomics Project citations

 (150)
library_books

Prediction of enhancer promoter interactions via natural language processing

2018
BMC Genomics
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] r datasets were adapted from TargetFinder. Promoter and enhancer regions were identified using ENCODE Segway [] and ChromHMM [] annotations for K562, GM12878, HeLa-S3, and HUVEC cell lines, and using Roadmap [] Epigenomics ChromHMM annotations for NHEK and IMR90 cell lines. Since EPIs could only happen between active enhancers and promoters, we used the full set of all enhancers and promoters as e […]

library_books

A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late Onset Alzheimer’s Disease

2018
Genetics
PMCID: 5937180
PMID: 29507048
DOI: 10.1534/genetics.117.300673

[…] lly, these final two SNPs are 8097 and 8292 bp downstream of PRKAR1B, and 21,254 and 21,059 bp upstream of PDGFA, respectively. To assess the functional relevance of the four variants, we queried the Roadmap Epigenomics () and ENCODE () resources using HaploReg () for chromatin state and protein binding annotations. We found that rs10490263 lies in promoter-associated histone marks in the hippocam […]

library_books

A catalog of potential putative functional variants in psoriasis genome wide association regions

2018
PLoS One
PMCID: 5929547
PMID: 29715312
DOI: 10.1371/journal.pone.0196635

[…] mented an enrichment test through variant set enrichment (VSE) R package []. We identified 26 types of human primary cells/cell lines, mainly primary immune cells and skin keratinocytes cells, in NIH Roadmap Epigenomics Consortium. They have been widely suggested to be relevant to the pathophysiology of psoriasis. We then downloaded the consolidated narrow peaks data of five core histone marks for […]

library_books

Highly similar genomic landscapes in monoclonal B cell lymphocytosis and ultra stable chronic lymphocytic leukemia with low frequency of driver mutations

2018
Haematologica
PMCID: 5927998
PMID: 29449433
DOI: 10.3324/haematol.2017.177212

[…] upplementary Figure S1).Funseq2, a bioinformatics tool investigating the linkage between NCVs and target genes using integrated bisulfite sequencing, ChIP-Sequencing, and RNA-sequencing data from the Roadmap Epigenomics Project, was used for the examination of the NCVs. This analysis revealed a total of 1517 variants in the MBL/CLL samples and 39 in the PMN samples. After stringent filtering, 106 […]

library_books

Epigenetic landscape influences the liver cancer genome architecture

2018
Nat Commun
PMCID: 5915380
PMID: 29691395
DOI: 10.1038/s41467-018-03999-y

[…] was covered by at least five reads. Epigenomic segments of the genome were identified using the 15 epigenomic segments defined in the HepG2 hepatoblastoma cell line or human adult liver cells by the Roadmap Epigenomics Consortium (Supplementary Fig. ) and plotted using the gplots package in R (https://cran.r-project.org/web/packages/gplots/index.html). […]

library_books

Selection on the regulation of sympathetic nervous activity in humans and chimpanzees

2018
PLoS Genet
PMCID: 5908061
PMID: 29672586
DOI: 10.1371/journal.pgen.1007311

[…] d, Neurosphere cortex-derived, Substantia nigra, Mid frontal lobe, Inferior temporal lobe, Hippocampus middle, Cingulate gyrus, Anterior caudate, and Angular gyrus). These data were obtained from the Roadmap Epigenomics project (http://www.roadmapepigenomics.org). HOMER (http://homer.ucsd.edu/homer/ngs/index.html) was run with the “–style histone” option to identify histone modification peaks. Add […]

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